| Next changeset 1:ae8de756dfcf (2019-12-16) |
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Commit message:
planemo upload commit 131562ad89c33a2f87754936ce3c8fe6899484c0 |
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added:
README.rst ipo4retgroup.r ipo4retgroup.xml ipo4xcmsSet.r ipo4xcmsSet.xml lib.r macros.xml planemo_test.sh repository_dependencies.xml test-data/MM-xset-merge.RData test-data/MM14.mzML test-data/MM14_IPO_ipo4xcmsSet.RData test-data/MM14_IPO_parameters4xcmsSet_peakwidth.tsv test-data/MM14_IPO_parameters4xcmsSet_ppm.tsv test-data/MM8.mzML test-data/MM_IPO_parameters4retgroup.tsv test-data/faahKO.xset.RData test-data/faahKO.xset.RData2 test-data/faahKO_IPO_parameters4retgroup.tsv test-data/faahKO_IPO_parameters4retgroup_bw.tsv test-data/faahKO_IPO_parameters4retgroup_mzmid.tsv test-data/faahKO_reduce.zip test-data/sacuri_2files.zip test-data/sacuri_2files_centWave_IPO_parameters4xcmsSet.tsv test-data/sacuri_2files_matchedFilter_IPO_parameters4xcmsSet.tsv |
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| diff -r 000000000000 -r ac5f2936575b README.rst --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README.rst Thu Aug 03 06:00:00 2017 -0400 |
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| @@ -0,0 +1,14 @@ + +Changelog/News +-------------- + +**Version X.X.X - XX/XX/XXXX** + +- NEW: + +Test Status +----------- + +Planemo test using conda: failed on the faahKO_reduce.zip + +Planemo shed_test : unbuild |
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| diff -r 000000000000 -r ac5f2936575b ipo4retgroup.r --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/ipo4retgroup.r Thu Aug 03 06:00:00 2017 -0400 |
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| @@ -0,0 +1,158 @@ +#!/usr/bin/env Rscript +#Authors Gildas Le Corguille and Yann Guitton + + +# ----- LOG FILE ----- +log_file=file("log.txt", open = "wt") +sink(log_file) +sink(log_file, type = "output") + + +# ----- PACKAGE ----- +options(bitmapType='cairo') +cat("\tPACKAGE INFO\n") +#pkgs=c("xcms","batch") +pkgs=c("parallel","BiocGenerics", "Biobase", "Rcpp", "mzR", "xcms","rsm","igraph","CAMERA","IPO","snow","batch") +for(pkg in pkgs) { + suppressWarnings( suppressPackageStartupMessages( stopifnot( library(pkg, quietly=TRUE, logical.return=TRUE, character.only=TRUE)))) + cat(pkg,"\t",as.character(packageVersion(pkg)),"\n",sep="") +} +source_local <- function(fname){ argv <- commandArgs(trailingOnly = FALSE); base_dir <- dirname(substring(argv[grep("--file=", argv)], 8)); source(paste(base_dir, fname, sep="/")) } +cat("\n\n"); + + +# ----- ARGUMENTS ----- +cat("\tARGUMENTS INFO\n") +listArguments = parseCommandArgs(evaluate=FALSE) #interpretation of arguments given in command line as an R list of objects +write.table(as.matrix(listArguments), col.names=F, quote=F, sep='\t') + +cat("\n\n"); + + +# ----- ARGUMENTS PROCESSING ----- +cat("\tINFILE PROCESSING INFO\n") + +#image is an .RData file necessary to use xset variable given by previous tools +if (!is.null(listArguments[["image"]])){ + load(listArguments[["image"]]); listArguments[["image"]]=NULL +} + +#Import the different functions +source_local("lib.r") + +cat("\n\n") + +#Import the different functions + +# ----- PROCESSING INFILE ----- +cat("\tARGUMENTS PROCESSING INFO\n") + + +parametersOutput = "parametersOutput.tsv" +if (!is.null(listArguments[["parametersOutput"]])){ + parametersOutput = listArguments[["parametersOutput"]]; listArguments[["parametersOutput"]]=NULL +} + +samplebyclass = 2 +if (!is.null(listArguments[["samplebyclass"]])){ + samplebyclass = listArguments[["samplebyclass"]]; listArguments[["samplebyclass"]]=NULL +} + +#necessary to unzip .zip file uploaded to Galaxy +#thanks to .zip file it's possible to upload many file as the same time conserving the tree hierarchy of directories + + +if (!is.null(listArguments[["zipfile"]])){ + zipfile= listArguments[["zipfile"]]; listArguments[["zipfile"]]=NULL +} + + +if (!is.null(listArguments[["singlefile_galaxyPath"]])){ + singlefile_galaxyPath = unlist(strsplit(listArguments[["singlefile_galaxyPath"]],",")); listArguments[["singlefile_galaxyPath"]]=NULL + singlefile_sampleName = unlist(strsplit(listArguments[["singlefile_sampleName"]],",")); listArguments[["singlefile_sampleName"]]=NULL +} + +# single file case +#@TODO: need to be refactoring +if(exists("singlefile_galaxyPath") && (singlefile_galaxyPath!="")) { + + cwd=getwd() + dir.create("raw") + setwd("raw") + + for (singlefile_galaxyPath_i in seq(1:length(singlefile_galaxyPath))) { + if(!file.exists(singlefile_galaxyPath[singlefile_galaxyPath_i])){ + error_message=paste("Cannot access the sample:",singlefile_sampleName[singlefile_galaxyPath_i],"located:",singlefile_galaxyPath[singlefile_galaxyPath_i],". Please, contact your administrator ... if you have one!") + print(error_message); stop(error_message) + } + file.symlink(singlefile_galaxyPath[singlefile_galaxyPath_i],singlefile_sampleName[singlefile_galaxyPath_i]) + } + + setwd(cwd) + + directory = "raw" + +} + +# We unzip automatically the chromatograms from the zip files. +if(exists("zipfile") && (zipfile!="")) { + if(!file.exists(zipfile)){ + error_message=paste("Cannot access the Zip file:",zipfile,". Please, contact your administrator ... if you have one!") + print(error_message) + stop(error_message) + } + + #list all file in the zip file + #zip_files=unzip(zipfile,list=T)[,"Name"] + + # Because IPO only want raw data in its working directory + dir.create("ipoworkingdir") + setwd("ipoworkingdir") + + #unzip + suppressWarnings(unzip(zipfile, unzip="unzip")) + + #get the directory name + filesInZip=unzip(zipfile, list=T); + directories=unique(unlist(lapply(strsplit(filesInZip$Name,"/"), function(x) x[1]))); + directories=directories[!(directories %in% c("__MACOSX")) & file.info(directories)$isdir] + directory = "." + if (length(directories) == 1) directory = directories + + cat("files_root_directory\t",directory,"\n") + + +} + +#addition of the directory to the list of arguments in the first position +checkXmlStructure(directory) +checkFilesCompatibilityWithXcms(directory) + +cat("\n\n") + + + + + + +# ----- MAIN PROCESSING INFO ----- +cat("\tMAIN PROCESSING INFO\n") + + +ipo4retgroup(xset, directory, parametersOutput, listArguments, samplebyclass) + + + +cat("\n\n") + + +# ----- EXPORT ----- + +cat("\tEXPORTING INFO\n") + +#save.image(file="ipo-retcor.RData") + +cat("\n\n") + + +cat("\tDONE\n") |
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| diff -r 000000000000 -r ac5f2936575b ipo4retgroup.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/ipo4retgroup.xml Thu Aug 03 06:00:00 2017 -0400 |
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| b'@@ -0,0 +1,364 @@\n+<tool id="ipo4retgroup" name="IPO for group and retcor" version="0.0.1">\n+\n+ <description>IPO optimization process for xcms.group and xcms.retcor</description>\n+\n+ <macros>\n+ <import>macros.xml</import>\n+\n+ <macro name="group_density_bw_fixed">\n+ <param name="bw" type="integer" value="30" label="Bandwidth" help="[bw] bandwidth (standard deviation or half width at half maximum) of gaussian smoothing kernel to apply to the peak density chromatogram" />\n+ </macro>\n+\n+ <macro name="group_density_mzwid_fixed">\n+ <param name="mzwid" type="float" value="0.25" label="Width of overlapping m/z slices" help="[mzwid] to use for creating peak density chromatograms and grouping peaks across samples " />\n+ </macro>\n+ </macros>\n+\n+ <expand macro="requirements"/>\n+ <expand macro="stdio"/>\n+\n+ <command><![CDATA[\n+ LANG=C Rscript $__tool_directory__/ipo4retgroup.r\n+\n+ image \'$image\'\n+\n+ parametersOutput \'$parametersOutput\'\n+\n+ samplebyclass $samplebyclass\n+\n+ @COMMAND_NSLAVES@\n+\n+ ## group methods\n+\n+ sleep 0.001\n+ #if $group.methods.method == "density":\n+ bw "c($group.methods.section_group_density_optiomizable.conditional_parameter.bw)"\n+ mzwid "c($group.methods.section_group_density_optiomizable.conditional_parameter.mzwid)"\n+\n+ minfrac $group.methods.section_group_density_non_optimizable.minfrac\n+ max $group.methods.section_group_density_non_optimizable.max\n+ #end if\n+\n+ ## retcor methods\n+\n+ #if $retcor.methods.method == "obiwarp":\n+ retcorMethod obiwarp\n+ profStep $methods.section_retcor_obiwarp_non_optimizable.profStep\n+\n+ #elif $retcor.methods.method == "peakgroups":\n+ retcorMethod loess\n+ smooth $retcor.methods.section_retcor_peakgroups_non_optimizable.smooth\n+ extra $retcor.methods.section_retcor_peakgroups_non_optimizable.extra\n+ missing $retcor.methods.section_retcor_peakgroups_non_optimizable.missing\n+ span $retcor.methods.section_retcor_peakgroups_non_optimizable.span\n+ family $retcor.methods.section_retcor_peakgroups_non_optimizable.family\n+ plottype $retcor.methods.section_retcor_peakgroups_non_optimizable.plottype\n+ #elif $retcor.methods.method == "none":\n+ retcorMethod none\n+ #end if\n+\n+ @COMMAND_FILE_LOAD@\n+\n+ @COMMAND_LOG_EXIT@\n+ ]]></command>\n+\n+ <inputs>\n+\n+ <param name="image" type="data" format="rdata.xcms.raw,rdata.xcms.group,rdata.xcms.retcor,rdata" label="xset RData file" help="output file from another function xcms (xcmsSet, retcor etc.)" />\n+\n+ <param name="samplebyclass" type="integer" value="2" label="Number of samples used per class to estimate the best parameters" help="Set to 0 to use the whole dataset. To save time, reduce this number" />\n+\n+ <section name="group" title="Group Options" expanded="True">\n+ <conditional name="methods">\n+ <param name="method" type="select" label="Method to use for grouping" help="[method] See the help section below. Only the density method is available so far">\n+ <option value="density" selected="true">density</option>\n+ </param>\n+ <when value="density">\n+ <section name="section_group_density_optiomizable" title="Optimizable parameters" expanded="True">\n+ <conditional name="conditional_parameter">\n+ <param name="select_parameter" type="select" label="Which parameter do you want to optimize?" help="Only one paramter can be optimized at once. The other will require fixed values">\n+ <option value="bw">Bandwidth [bw]</option>\n+ <option value="mzwid">Width of overlapping m/z slices [mzwid]</option>\n+ '..b'======= =========\n+Name output file format parameter\n+========================= ================= ======= =========\n+NA NA zip NA\n+========================= ================= ======= =========\n+\n+\n+**Downstream tools**\n+\n++---------------------------+----------------------+-----------------+\n+| Name | Output file | Format |\n++===========================+======================+=================+\n+|xcms.xcmsSet | parametersOutput.tsv | Tabular |\n++---------------------------+--------------------+-------------------+\n+\n+\n+\n+-----------\n+Input files\n+-----------\n+\n++---------------------------+------------+\n+| Parameter : num + label | Format |\n++===========================+============+\n+| 1 : Choose your inputs | zip |\n++---------------------------+------------+\n+\n+**Choose your inputs**\n+\n+You have two methods for your inputs:\n+\n+ | Zip file (recommended): You can put a zip file containing your inputs: myinputs.zip (containing all your conditions as sub-directories).\n+ | library folder: You must specify the name of your "library" (folder) created within your space project (for example: /projet/externe/institut/login/galaxylibrary/yourlibrary). Your library must contain all your conditions as sub-directories.\n+\n+Steps for creating the zip file\n+-------------------------------\n+\n+**Step1: Creating your directory and hierarchize the subdirectories**\n+\n+\n+VERY IMPORTANT: If you zip your files under Windows, you must use the 7Zip software (http://www.7-zip.org/), otherwise your zip will not be well unzipped on the platform W4M (zip corrupted bug).\n+\n+Your zip should contain all your conditions as sub-directories. For example, two conditions (mutant and wild):\n+arabidopsis/wild/01.raw\n+arabidopsis/mutant/01.raw\n+\n+**Step2: Creating a zip file**\n+\n+Create your zip file (e.g.: arabidopsis.zip).\n+\n+**Step 3 : Uploading it to our Galaxy server**\n+\n+If your zip file is less than 2Gb, you get use the Get Data tool to upload it.\n+\n+Otherwise if your zip file is larger than 2Gb, please refer to the HOWTO on workflow4metabolomics.org (http://application.sb-roscoff.fr/download/w4m/howto/galaxy_upload_up_2Go.pdf).\n+\n+For more informations, don\'t hesitate to send us an email at supportATworkflow4metabolomics.org).\n+\n+Advices for converting your files for the XCMS input\n+----------------------------------------------------\n+\n+We recommend you to convert your raw files to **mzXML** in centroid mode (smaller files) and the files will be compatible with the xmcs centWave method.\n+\n+**We recommend you the following parameters:**\n+\n+Use Filtering: **True**\n+\n+Use Peak Picking: **True**\n+\n+Peak Peaking -Apply to MS Levels: **All Levels (1-)** : Centroid Mode\n+\n+Use zlib: **64**\n+\n+Binary Encoding: **64**\n+\n+m/z Encoding: **64**\n+\n+Intensity Encoding: **64**\n+\n+\n+----------\n+Parameters\n+----------\n+\n+Extraction method for peaks detection\n+-------------------------------------\n+\n+**Matched Filter**\n+\n+ | One parameter to consider is the Gaussian model peak width used for matched filtration,an integral part of the peak detection algorithm.\n+ | For a discussion of how model peak width affects the signal to noise ratio, see Danielsson et al. (2002).\n+\n+\n+**cent Wave**\n+\n+ | This algorithm is most suitable for high resolution LC/{TOF,OrbiTrap,FTICR}-MS data in centroid mode.\n+ | Due to the fact that peak centroids are used, a binning step is not necessary.\n+ | The method is capable of detecting close-by-peaks and also overlapping peaks. Some efforts are made to detect the exact peak boundaries to get precise peak integrals.\n+\n+\n+------------\n+Output files\n+------------\n+\n+IPO_parameters4xcmsSet.tsv\n+\n+ | Optimal parameters for xcmsSet\n+\n+\n+---------------------------------------------------\n+\n+Changelog/News\n+--------------\n+\n+\n+\n+ ]]></help>\n+\n+ <expand macro="citation" />\n+</tool>\n' |
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| diff -r 000000000000 -r ac5f2936575b ipo4xcmsSet.r --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/ipo4xcmsSet.r Thu Aug 03 06:00:00 2017 -0400 |
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| @@ -0,0 +1,163 @@ +#!/usr/bin/env Rscript +#Authors Gildas Le Corguille and Yann Guitton + + +# ----- LOG FILE ----- +log_file=file("log.txt", open = "wt") +sink(log_file) +sink(log_file, type = "output") + + +# ----- PACKAGE ----- +options(bitmapType='cairo') +cat("\tPACKAGE INFO\n") +#pkgs=c("xcms","batch") +pkgs=c("parallel","BiocGenerics", "Biobase", "Rcpp", "mzR", "xcms","rsm","igraph","CAMERA","IPO","snow","batch") +for(pkg in pkgs) { + suppressWarnings( suppressPackageStartupMessages( stopifnot( library(pkg, quietly=TRUE, logical.return=TRUE, character.only=TRUE)))) + cat(pkg,"\t",as.character(packageVersion(pkg)),"\n",sep="") +} +source_local <- function(fname){ argv <- commandArgs(trailingOnly = FALSE); base_dir <- dirname(substring(argv[grep("--file=", argv)], 8)); source(paste(base_dir, fname, sep="/")) } +cat("\n\n"); + + + + + +# ----- ARGUMENTS ----- +cat("\tARGUMENTS INFO\n") +listArguments = parseCommandArgs(evaluate=FALSE) #interpretation of arguments given in command line as an R list of objects +write.table(as.matrix(listArguments), col.names=F, quote=F, sep='\t') + +cat("\n\n"); + + +# ----- ARGUMENTS PROCESSING ----- +cat("\tINFILE PROCESSING INFO\n") + + +#Import the different functions +source_local("lib.r") + +cat("\n\n") + +#Import the different functions + +# ----- PROCESSING INFILE ----- +cat("\tARGUMENTS PROCESSING INFO\n") + +xsetRdataOutput = paste("ipo4xcmsSet","RData",sep=".") +if (!is.null(listArguments[["xsetRdataOutput"]])){ + xsetRdataOutput = listArguments[["xsetRdataOutput"]]; listArguments[["xsetRdataOutput"]]=NULL +} + +parametersOutput = "parametersOutput.tsv" +if (!is.null(listArguments[["parametersOutput"]])){ + parametersOutput = listArguments[["parametersOutput"]]; listArguments[["parametersOutput"]]=NULL +} + +samplebyclass = 2 +if (!is.null(listArguments[["samplebyclass"]])){ + samplebyclass = listArguments[["samplebyclass"]]; listArguments[["samplebyclass"]]=NULL +} + +#necessary to unzip .zip file uploaded to Galaxy +#thanks to .zip file it's possible to upload many file as the same time conserving the tree hierarchy of directories + + +if (!is.null(listArguments[["zipfile"]])){ + zipfile= listArguments[["zipfile"]]; listArguments[["zipfile"]]=NULL +} + + +if (!is.null(listArguments[["singlefile_galaxyPath"]])){ + singlefile_galaxyPath = listArguments[["singlefile_galaxyPath"]]; listArguments[["singlefile_galaxyPath"]]=NULL + singlefile_sampleName = listArguments[["singlefile_sampleName"]]; listArguments[["singlefile_sampleName"]]=NULL +} + +# single file case +#@TODO: need to be refactoring +if(exists("singlefile_galaxyPath") && (singlefile_galaxyPath!="")) { + if(!file.exists(singlefile_galaxyPath)){ + error_message=paste("Cannot access the sample:",singlefile_sampleName,"located:",singlefile_galaxyPath,". Please, contact your administrator ... if you have one!") + print(error_message); stop(error_message) + } + + cwd=getwd() + dir.create("raw") + setwd("raw") + file.symlink(singlefile_galaxyPath,singlefile_sampleName) + setwd(cwd) + + directory = "raw" + +} + +# We unzip automatically the chromatograms from the zip files. +if(exists("zipfile") && (zipfile!="")) { + if(!file.exists(zipfile)){ + error_message=paste("Cannot access the Zip file:",zipfile,". Please, contact your administrator ... if you have one!") + print(error_message) + stop(error_message) + } + + #list all file in the zip file + #zip_files=unzip(zipfile,list=T)[,"Name"] + + # Because IPO only want raw data in its working directory + dir.create("ipoworkingdir") + setwd("ipoworkingdir") + + #unzip + suppressWarnings(unzip(zipfile, unzip="unzip")) + + #get the directory name + filesInZip=unzip(zipfile, list=T); + directories=unique(unlist(lapply(strsplit(filesInZip$Name,"/"), function(x) x[1]))); + directories=directories[!(directories %in% c("__MACOSX")) & file.info(directories)$isdir] + directory = "." + if (length(directories) == 1) directory = directories + + cat("files_root_directory\t",directory,"\n") + + +} + +#addition of the directory to the list of arguments in the first position +checkXmlStructure(directory) +checkFilesCompatibilityWithXcms(directory) + +cat("\n\n") + + + + + + +# ----- MAIN PROCESSING INFO ----- +cat("\tMAIN PROCESSING INFO\n") + + +xset = ipo4xcmsSet(directory, parametersOutput, listArguments, samplebyclass) + + + +cat("\n\n") + + +# ----- EXPORT ----- + +cat("\tXSET OBJECT INFO\n") +print(xset) +#delete the parameters to avoid the passage to the next tool in .RData image + + +#saving R data in .Rdata file to save the variables used in the present tool +objects2save = c("xset","zipfile") +save(list=objects2save[objects2save %in% ls()], file=xsetRdataOutput) + +cat("\n\n") + + +cat("\tDONE\n") + |
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| diff -r 000000000000 -r ac5f2936575b ipo4xcmsSet.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/ipo4xcmsSet.xml Thu Aug 03 06:00:00 2017 -0400 |
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| b'@@ -0,0 +1,382 @@\n+<tool id="ipo4xcmsSet" name="IPO for xcmsSet" version="0.0.3">\n+\n+ <description>IPO optimization process for xcms.xcmsSet</description>\n+\n+ <macros>\n+ <import>macros.xml</import>\n+\n+ <macro name="centwave_ppm_fixed">\n+ <param name="ppm" type="integer" value="25" label="Max tolerated ppm m/z deviation in consecutive scans in ppm" help="[ppm]" />\n+ </macro>\n+ <macro name="centwave_peakwidth_fixed">\n+ <param name="min_peakwidth" type="float" value="20" label="Min peak width range in seconds" optional="true" help="[min_peakwidth]" />\n+ <param name="max_peakwidth" type="float" value="50" label="Max peak width range in seconds" optional="true" help="[max_peakwidth]" />\n+ </macro>\n+ <macro name="centwave_mzdiff_fixed">\n+ <param name="mzdiff" type="float" value="-0.001" label="Minimum difference in m/z for peaks with overlapping Retention Times" help="[mzdiff] Can be negative to allow overlap" />\n+ </macro>\n+\n+ <macro name="matchedfilter_fwhm_fixed">\n+ <param name="fwhm" type="integer" value="30" label="Full width at half maximum of matched filtration gaussian model peak" help="[fwhm] Only used to calculate the actual sigma" />\n+ </macro>\n+ <macro name="matchedfilter_mzdiff_fixed">\n+ <param name="mzdiff" type="float" value="0.6" label="Minimum difference in m/z for peaks with overlapping Retention Times" help="[mzdiff] By default: 0.8-step*steps " />\n+ </macro>\n+ </macros>\n+\n+ <expand macro="requirements"/>\n+ <expand macro="stdio"/>\n+\n+ <command><![CDATA[\n+ LANG=C Rscript $__tool_directory__/ipo4xcmsSet.r\n+\n+ #if $input.is_of_type("mzxml") or $input.is_of_type("mzml") or $input.is_of_type("mzdata") or $input.is_of_type("netcdf"):\n+ singlefile_galaxyPath \'$input\' singlefile_sampleName \'$input.name\'\n+ #else\n+ zipfile \'$input\'\n+ #end if\n+\n+ parametersOutput $parametersOutput\n+ xsetRdataOutput $xsetRData\n+\n+ samplebyclass $samplebyclass\n+\n+ ## profmethod $profmethod\n+ @COMMAND_NSLAVES@\n+ method $methods.method\n+ #if $methods.method == "centWave":\n+ ppm "c($methods.section_centwave_optiomizable.conditional_parameter.ppm)"\n+ min_peakwidth "c($methods.section_centwave_optiomizable.conditional_parameter.min_peakwidth)"\n+ max_peakwidth "c($methods.section_centwave_optiomizable.conditional_parameter.max_peakwidth)"\n+ mzdiff "c($methods.section_centwave_optiomizable.conditional_parameter.mzdiff)"\n+\n+ snthresh $methods.section_centwave_non_optiomizable.snthresh\n+ integrate $methods.section_centwave_non_optiomizable.integrate\n+ noise $methods.section_centwave_non_optiomizable.noise\n+ prefilter "c($methods.section_centwave_non_optiomizable.prefilter)"\n+\n+ #elif $methods.method == "matchedFilter":\n+ fwhm "c($methods.section_matchedfilter_optiomizable.conditional_parameter.fwhm)"\n+ mzdiff "c($methods.section_matchedfilter_optiomizable.conditional_parameter.mzdiff)"\n+\n+ step $methods.section_matchedfilter_non_optimizable.step\n+ steps $methods.section_matchedfilter_non_optimizable.steps\n+ max $methods.section_matchedfilter_non_optimizable.max\n+ snthresh $methods.section_matchedfilter_non_optimizable.snthresh\n+ #end if\n+\n+ @COMMAND_LOG_EXIT@\n+ ]]></command>\n+\n+ <inputs>\n+\n+ <param name="input" type="data" format="mzxml,mzml,mzdata,netcdf,no_unzip.zip,zip" 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." />\n+\n+ <param name="samplebyclass" type="integer" value="2" label="Number of samples used per class to estimate the best para'..b'======= =========\n+Name output file format parameter\n+========================= ================= ======= =========\n+NA NA zip NA\n+========================= ================= ======= =========\n+\n+\n+**Downstream tools**\n+\n++---------------------------+----------------------+-----------------+\n+| Name | Output file | Format |\n++===========================+======================+=================+\n+|xcms.xcmsSet | parametersOutput.tsv | Tabular |\n++---------------------------+--------------------+-------------------+\n+\n+\n+\n+-----------\n+Input files\n+-----------\n+\n++---------------------------+------------+\n+| Parameter : num + label | Format |\n++===========================+============+\n+| 1 : Choose your inputs | zip |\n++---------------------------+------------+\n+\n+**Choose your inputs**\n+\n+You have two methods for your inputs:\n+\n+ | Zip file (recommended): You can put a zip file containing your inputs: myinputs.zip (containing all your conditions as sub-directories).\n+ | library folder: You must specify the name of your "library" (folder) created within your space project (for example: /projet/externe/institut/login/galaxylibrary/yourlibrary). Your library must contain all your conditions as sub-directories.\n+\n+Steps for creating the zip file\n+-------------------------------\n+\n+**Step1: Creating your directory and hierarchize the subdirectories**\n+\n+\n+VERY IMPORTANT: If you zip your files under Windows, you must use the 7Zip software (http://www.7-zip.org/), otherwise your zip will not be well unzipped on the platform W4M (zip corrupted bug).\n+\n+Your zip should contain all your conditions as sub-directories. For example, two conditions (mutant and wild):\n+arabidopsis/wild/01.raw\n+arabidopsis/mutant/01.raw\n+\n+**Step2: Creating a zip file**\n+\n+Create your zip file (e.g.: arabidopsis.zip).\n+\n+**Step 3 : Uploading it to our Galaxy server**\n+\n+If your zip file is less than 2Gb, you get use the Get Data tool to upload it.\n+\n+Otherwise if your zip file is larger than 2Gb, please refer to the HOWTO on workflow4metabolomics.org (http://application.sb-roscoff.fr/download/w4m/howto/galaxy_upload_up_2Go.pdf).\n+\n+For more informations, don\'t hesitate to send us an email at supportATworkflow4metabolomics.org).\n+\n+Advices for converting your files for the XCMS input\n+----------------------------------------------------\n+\n+We recommend you to convert your raw files to **mzXML** in centroid mode (smaller files) and the files will be compatible with the xmcs centWave method.\n+\n+**We recommend you the following parameters:**\n+\n+Use Filtering: **True**\n+\n+Use Peak Picking: **True**\n+\n+Peak Peaking -Apply to MS Levels: **All Levels (1-)** : Centroid Mode\n+\n+Use zlib: **64**\n+\n+Binary Encoding: **64**\n+\n+m/z Encoding: **64**\n+\n+Intensity Encoding: **64**\n+\n+\n+----------\n+Parameters\n+----------\n+\n+Extraction method for peaks detection\n+-------------------------------------\n+\n+**Matched Filter**\n+\n+ | One parameter to consider is the Gaussian model peak width used for matched filtration,an integral part of the peak detection algorithm.\n+ | For a discussion of how model peak width affects the signal to noise ratio, see Danielsson et al. (2002).\n+\n+\n+**cent Wave**\n+\n+ | This algorithm is most suitable for high resolution LC/{TOF,OrbiTrap,FTICR}-MS data in centroid mode.\n+ | Due to the fact that peak centroids are used, a binning step is not necessary.\n+ | The method is capable of detecting close-by-peaks and also overlapping peaks. Some efforts are made to detect the exact peak boundaries to get precise peak integrals.\n+\n+\n+------------\n+Output files\n+------------\n+\n+IPO_parameters4xcmsSet.tsv\n+\n+ | Optimal parameters for xcmsSet\n+\n+\n+---------------------------------------------------\n+\n+Changelog/News\n+--------------\n+\n+\n+\n+ ]]></help>\n+\n+ <expand macro="citation" />\n+</tool>\n' |
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| diff -r 000000000000 -r ac5f2936575b lib.r --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/lib.r Thu Aug 03 06:00:00 2017 -0400 |
| [ |
| @@ -0,0 +1,120 @@ +## +## This function launch IPO functions to get the best parameters for xcmsSet +## A sample among the whole dataset is used to save time +## +ipo4xcmsSet = function(directory, parametersOutput, listArguments, samplebyclass=4) { + setwd(directory) + + files = list.files(".", recursive=T) # "KO/ko15.CDF" "KO/ko16.CDF" "WT/wt15.CDF" "WT/wt16.CDF" + files_classes = basename(dirname(files)) # "KO", "KO", "WT", "WT" + + mzmlfile = files + if (samplebyclass > 0) { + #random selection of N files for IPO in each class + classes<-unique(basename(dirname(files))) + mzmlfile = NULL + for (class_i in classes){ + files_class_i = files[files_classes==class_i] + if (samplebyclass > length(files_class_i)) { + mzmlfile = c(mzmlfile, files_class_i) + } else { + mzmlfile = c(mzmlfile,sample(files_class_i,samplebyclass)) + } + } + } + #@TODO: else, must we keep the RData to been use directly by group? + + cat("\t\tSamples used:\n") + print(mzmlfile) + + peakpickingParameters = getDefaultXcmsSetStartingParams(listArguments[["method"]]) #get default parameters of IPO + + # filter listArguments to only get releavant parameters and complete with those that are not declared + peakpickingParametersUser = c(listArguments[names(listArguments) %in% names(peakpickingParameters)], peakpickingParameters[!(names(peakpickingParameters) %in% names(listArguments))]) + peakpickingParametersUser$verbose.columns = TRUE + + #peakpickingParametersUser$profparam <- list(step=0.005) #not yet used by IPO have to think of it for futur improvement + resultPeakpicking = optimizeXcmsSet(mzmlfile, peakpickingParametersUser, nSlaves=peakpickingParametersUser$nSlaves, subdir="../IPO_results") #some images generated by IPO + + # export + resultPeakpicking_best_settings_parameters = resultPeakpicking$best_settings$parameters[!(names(resultPeakpicking$best_settings$parameters) %in% c("nSlaves","verbose.columns"))] + write.table(t(as.data.frame(resultPeakpicking_best_settings_parameters)), file=parametersOutput, sep="\t", row.names=T, col.names=F, quote=F) #can be read by user + + return (resultPeakpicking$best_settings$xset) +} + +## +## This function launch IPO functions to get the best parameters for group and retcor +## +ipo4retgroup = function(xset, directory, parametersOutput, listArguments, samplebyclass=4) { + setwd(directory) + + files = list.files(".", recursive=T) # "KO/ko15.CDF" "KO/ko16.CDF" "WT/wt15.CDF" "WT/wt16.CDF" + files_classes = basename(dirname(files)) # "KO", "KO", "WT", "WT" + + retcorGroupParameters = getDefaultRetGroupStartingParams(listArguments[["retcorMethod"]]) #get default parameters of IPO + print(retcorGroupParameters) + # filter listArguments to only get releavant parameters and complete with those that are not declared + retcorGroupParametersUser = c(listArguments[names(listArguments) %in% names(retcorGroupParameters)], retcorGroupParameters[!(names(retcorGroupParameters) %in% names(listArguments))]) + print("retcorGroupParametersUser") + print(retcorGroupParametersUser) + resultRetcorGroup = optimizeRetGroup(xset, retcorGroupParametersUser, nSlaves=listArguments[["nSlaves"]], subdir="../IPO_results") #some images generated by IPO + + # export + resultRetcorGroup_best_settings_parameters = resultRetcorGroup$best_settings + write.table(t(as.data.frame(resultRetcorGroup_best_settings_parameters)), file=parametersOutput, sep="\t", row.names=T, col.names=F, quote=F) #can be read by user +} + + + + +## +## This function check if xcms will found all the files +## +#@author Gildas Le Corguille lecorguille@sb-roscoff.fr ABiMS TEAM +checkFilesCompatibilityWithXcms <- function(directory) { + cat("Checking files filenames compatibilities with xmcs...\n") + # WHAT XCMS WILL FIND + filepattern <- c("[Cc][Dd][Ff]", "[Nn][Cc]", "([Mm][Zz])?[Xx][Mm][Ll]","[Mm][Zz][Dd][Aa][Tt][Aa]", "[Mm][Zz][Mm][Ll]") + filepattern <- paste(paste("\\.", filepattern, "$", sep = ""),collapse = "|") + info <- file.info(directory) + listed <- list.files(directory[info$isdir], pattern = filepattern,recursive = TRUE, full.names = TRUE) + files <- c(directory[!info$isdir], listed) + files_abs <- file.path(getwd(), files) + exists <- file.exists(files_abs) + files[exists] <- files_abs[exists] + files[exists] <- sub("//","/",files[exists]) + + # WHAT IS ON THE FILESYSTEM + filesystem_filepaths=system(paste("find $PWD/",directory," -not -name '\\.*' -not -path '*conda-env*' -type f -name \"*\"", sep=""), intern=T) + filesystem_filepaths=filesystem_filepaths[grep(filepattern, filesystem_filepaths, perl=T)] + + # COMPARISON + if (!is.na(table(filesystem_filepaths %in% files)["FALSE"])) { + write("\n\nERROR: List of the files which will not be imported by xcmsSet",stderr()) + write(filesystem_filepaths[!(filesystem_filepaths %in% files)],stderr()) + stop("\n\nERROR: One or more of your files will not be import by xcmsSet. It may due to bad characters in their filenames.") + + } +} + + + +## +## This function check if XML contains special caracters. It also checks integrity and completness. +## +#@author Misharl Monsoor misharl.monsoor@sb-roscoff.fr ABiMS TEAM +checkXmlStructure <- function (directory) { + cat("Checking XML structure...\n") + + cmd=paste("IFS=$'\n'; for xml in $(find",directory,"-not -name '\\.*' -not -path '*conda-env*' -type f -iname '*.*ml*'); do if [ $(xmllint --nonet --noout \"$xml\" 2> /dev/null; echo $?) -gt 0 ]; then echo $xml;fi; done;") + capture=system(cmd,intern=TRUE) + + if (length(capture)>0){ + #message=paste("The following mzXML or mzML file is incorrect, please check these files first:",capture) + write("\n\nERROR: The following mzXML or mzML file(s) are incorrect, please check these files first:", stderr()) + write(capture, stderr()) + stop("ERROR: xcmsSet cannot continue with incorrect mzXML or mzML files") + } + +} |
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| diff -r 000000000000 -r ac5f2936575b macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Thu Aug 03 06:00:00 2017 -0400 |
| [ |
| @@ -0,0 +1,103 @@ +<?xml version="1.0"?> +<macros> + <xml name="requirements"> + <requirements> + <requirement type="package" version="0.4_1">r-snow</requirement> + <requirement type="package" version="1.0.0">bioconductor-ipo</requirement> + <requirement type="package" version="1.1_4">r-batch</requirement> + </requirements> + </xml> + <xml name="stdio"> + <stdio> + <exit_code range="1" level="fatal" /> + </stdio> + </xml> + + <token name="@COMMAND_SCRIPT@"> + LANG=C Rscript $__tool_directory__/ + </token> + + <token name="@COMMAND_LOG_EXIT@"> + ; + return=\$?; + mv log.txt $log; + cat $log; + sh -c "exit \$return" + </token> + + <token name="@COMMAND_NSLAVES@"> + nSlaves \${GALAXY_SLOTS:-1} + </token> + + <!-- zipfile load for planemo test --> + + <token name="@COMMAND_FILE_LOAD@"> + #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 $file_load_section.file_load_conditional.input ] ) + + singlefile_galaxyPath '$singlefile_galaxyPath' singlefile_sampleName '$singlefile_sampleName' + #else + zipfile '$file_load_section.file_load_conditional.input' + #end if + #end if + </token> + + <xml name="input_file_load"> + <section name="file_load_section" title="Resubmit your raw dataset or your zip file"> + <conditional name="file_load_conditional"> + <param name="file_load_select" type="select" label="Resubmit your dataset or your zip file" help="Use only if you get a message which say that your original dataset or zip file have been deleted on the server." > + <option value="no" >no need</option> + <option value="yes" >yes</option> + </param> + <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." /> + </when> + </conditional> + </section> + </xml> + + <xml name="test_file_load_zip"> + <section name="file_load_section"> + <conditional name="file_load_conditional"> + <param name="file_load_select" value="yes" /> + <param name="input" value="faahKO_reduce.zip" ftype="zip" /> + </conditional> + </section> + </xml> + + <xml name="test_file_load_single"> + <section name="file_load_section"> + <conditional name="file_load_conditional"> + <param name="file_load_select" value="yes" /> + <param name="input" value="wt15.CDF,ko16.CDF,ko15.CDF,wt16.CDF" ftype="netcdf" /> + </conditional> + </section> + </xml> + + <token name="@HELP_AUTHORS@"> +.. class:: infomark + +**Authors** Gunnar Libiseller, Michaela Dvorzak, Ulrike Kleb, Edgar Gander, Tobias Eisenberg, Frank Madeo, Steffen Neumann, Gert Trausinger, Frank Sinner, Thomas Pieber and Christoph Magnes + +.. class:: infomark + +**Galaxy integration** ABiMS TEAM - UPMC/CNRS - Station biologique de Roscoff and Yann Guitton yann.guitton@oniris-nantes.fr - part of Workflow4Metabolomics.org [W4M] + + | Contact support@workflow4metabolomics.org for any questions or concerns about the Galaxy implementation of this tool. + +--------------------------------------------------- + + </token> + + + <xml name="citation"> + <citations> + <citation type="doi">10.1186/s12859-015-0562-8</citation> + <citation type="doi">10.1093/bioinformatics/btu813</citation> + </citations> + </xml> +</macros> |
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| diff -r 000000000000 -r ac5f2936575b planemo_test.sh --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/planemo_test.sh Thu Aug 03 06:00:00 2017 -0400 |
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| @@ -0,0 +1,11 @@ +conda create -n r-ipo --use-local r-ipo r-batch +. ~/miniconda2/bin/activate r-ipo +planemo test --install_galaxy --galaxy_branch "dev" --update_test_data + + +# -- Use of conda dependencies +planemo conda_init --conda_prefix /tmp/mc +planemo conda_install --conda_prefix /tmp/mc . +planemo test --install_galaxy --conda_prefix /tmp/mc --conda_dependency_resolution + +planemo test --conda_auto_init --conda_auto_install --conda_dependency_resolution --conda_prefix /tmp/mc --galaxy_branch dev > planemo.out 2>&1 |
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| diff -r 000000000000 -r ac5f2936575b repository_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/repository_dependencies.xml Thu Aug 03 06:00:00 2017 -0400 |
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| @@ -0,0 +1,4 @@ +<?xml version="1.0"?> +<repositories> + <repository changeset_revision="7800ba9a4c1e" name="no_unzip_datatype" owner="lecorguille" toolshed="https://toolshed.g2.bx.psu.edu" /> +</repositories> |
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| diff -r 000000000000 -r ac5f2936575b test-data/MM-xset-merge.RData |
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| Binary file test-data/MM-xset-merge.RData has changed |
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| diff -r 000000000000 -r ac5f2936575b test-data/MM14.mzML --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/MM14.mzML Thu Aug 03 06:00:00 2017 -0400 |
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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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