| Previous changeset 11:91311aa08cdc (2017-01-30) Next changeset 13:c934dd5c49a9 (2017-11-29) |
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Commit message:
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 |
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modified:
README.rst abims_xcms_xcmsSet.xml lib.r macros.xml xcms.r |
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added:
destinations_input_type.py job_conf.xml.sample static/images/xcms_xcmsset_workflow.png test-data/HU_neg_017.mzXML test-data/MM14.mzML test-data/MM8.mzML |
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removed:
Makefile planemo_test.sh static/images/XCMS_Galaxy_workflow.png tool_dependencies.xml |
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| diff -r 91311aa08cdc -r 15646e937936 Makefile --- a/Makefile Mon Jan 30 08:52:59 2017 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,23 +0,0 @@ -# USAGE: make [install|clean] - -# -------- VARIABLE -------- - -OBJ=xcms_set.tgz -DEP=abims_xcms_xcmsSet.xml tool_dependencies.xml repository_dependencies.xml static test-data - - -# ------------------------ - -all: $(OBJ) - -$(OBJ): $(DEP) - tar --exclude=".svn" -zchf $@ $^ - -# ------------------------ - -install: $(OBJ) - mv *.tgz ~ - -clean: - rm *.tgz - |
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| diff -r 91311aa08cdc -r 15646e937936 README.rst --- a/README.rst Mon Jan 30 08:52:59 2017 -0500 +++ b/README.rst Fri Apr 07 07:35:01 2017 -0400 |
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| @@ -1,7 +1,33 @@ +Job Dynamic Destination Mapping +------------------------------- + +**Why** + +xcmsSet wrapper allow both individual file and zip file which can contain several samples. +Thus, it can be interesting to adjust the number of thread according to the input type. +For example: 1 thread for a single mzXML or NetCDF file and 8 threads for a zip file. + +**What** + +The [Dynamic Destination Mapping](https://galaxyproject.org/admin/config/jobs/#dynamic-destination-mapping) allow Galaxy to choose a destination at runtime based on factors such as the job inputs, user submitting the job, cluster status, etc... + +**How** + + - The file `destinations_input_type.py` (shiped with this tool) must be place in `lib/galaxy/jobs/rules/` + - The `job_conf.xml` must be inspired by the `job_conf.xml.sample` shiped with this tool + - The final destination names must match between the `job_conf.xml` and the `destinations_input_type.py` + - Restart Galaxy + Changelog/News -------------- +**Version 2.1.0 - 22/02/2017** + +- NEW: The W4M tools will be able now to take as input a single file. It will allow to submit in parallel several files and merge them afterward using "xcms.xcmsSet Merger" before "xcms.group". + +- BUGFIX: the default value of "matchedFilter" -> "Step size to use for profile generation" which was of 0.01 have been changed to fix with the XMCS default values to 0.1 + **Version 2.0.11 - 22/12/2016** - BUGFIX: propose scanrange for all methods @@ -49,13 +75,3 @@ - IMPROVEMENT: new datatype/dataset formats (rdata.xcms.raw, rdata.xcms.group, rdata.xcms.retcor ...) will facilitate the sequence of tools and so avoid incompatibility errors. - IMPROVEMENT: parameter labels have changed to facilitate their reading. - - -Test Status ------------ - -Planemo test using conda: passed - -Planemo test using source env.sh: passed - -Planemo shed_test : passed |
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| diff -r 91311aa08cdc -r 15646e937936 abims_xcms_xcmsSet.xml --- a/abims_xcms_xcmsSet.xml Mon Jan 30 08:52:59 2017 -0500 +++ b/abims_xcms_xcmsSet.xml Fri Apr 07 07:35:01 2017 -0400 |
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| b'@@ -1,5 +1,4 @@\n-<tool id="abims_xcms_xcmsSet" name="xcms.xcmsSet" version="2.0.11">\n-\n+<tool id="abims_xcms_xcmsSet" name="xcms.xcmsSet" version="2.1.0">\n <description>Filtration and Peak Identification using xcmsSet function from xcms R package to preprocess LC/MS data for relative quantification and statistical analysis </description>\n \n <macros>\n@@ -11,18 +10,19 @@\n \n <command><![CDATA[\n @COMMAND_XCMS_SCRIPT@\n- #if $inputs.input == "lib":\n- library $__app__.config.user_library_import_dir/$__user_email__/$inputs.library\n- #elif $inputs.input == "zip_file":\n- zipfile $inputs.zip_file\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 xfunction xcmsSet\n \n- xsetRdataOutput $xsetRData\n- sampleMetadataOutput $sampleMetadata\n- ticspdf $ticsRawPdf\n- bicspdf $bpcsRawPdf\n+ xsetRdataOutput \'$xsetRData\'\n+ sampleMetadataOutput \'$sampleMetadata\'\n+ ticspdf \'$ticsRawPdf\'\n+ bicspdf \'$bpcsRawPdf\'\n \n \n #if $options_scanrange.option == "show":\n@@ -48,9 +48,8 @@\n ## sigma "$methods.options_m.sigma"\n max $methods.options_m.max\n snthresh $methods.options_m.snthresh\n- ## mzdiff $methods.options_m.mzdiff\n steps $methods.options_m.steps\n- ## sleep $methods.options_m.sleep\n+ mzdiff $methods.options_m.mzdiff\n #end if\n #elif $methods.method == "MSW":\n snthr $methods.snthr\n@@ -65,21 +64,7 @@\n \n <inputs>\n \n- <conditional name="inputs">\n- <param name="input" type="select" label="Choose your inputs method" >\n- <option value="zip_file" selected="true">Zip file from your history containing your chromatograms</option>\n- <option value="lib" >Library directory name</option>\n- </param>\n- <when value="zip_file">\n- <param name="zip_file" type="data" format="no_unzip.zip,zip" label="Zip file" />\n- </when>\n- <when value="lib">\n- <param name="library" type="text" size="40" label="Library directory name" help="The name of your directory containing all your data" >\n- <validator type="empty_field"/>\n- </param>\n- </when>\n-\n- </conditional>\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 <conditional name="options_scanrange">\n <param name="option" type="select" label="Scan range option " >\n@@ -103,7 +88,6 @@\n <option value="binlinbase">binlinbase</option>\n <option value="intlin">intlin</option>\n </param>\n- <param name="nSlaves" type="integer" value="9" label="MPI-slaves CPU" help="number of MPI-slaves to use for parallel peak detection" />\n -->\n <conditional name="methods">\n <param name="method" type="select" label="Extraction method for peaks detection" help="[method] See the help section below">\n@@ -116,7 +100,7 @@\n <when value="centWave">\n <param name="ppm" type="integer" value="25" label="Max tolerated ppm m/z deviation in consecutive scans in ppm" help="[ppm]" />\n <param name="peakwidth" type="text" value="20,50" label="Min,Max peak width in seconds" help="[peakwidth]" />\n- \n+\n <conditional name="options_c">\n <param name="option" type="select" label="Advanced options" >\n '..b'ds|method" value="centWave" />\n+ <param name="methods|ppm" value="25" />\n+ <param name="methods|peakwidth" value="20,50" />\n+ <output name="log">\n+ <assert_contents>\n+ <has_text text="object with 1 samples" />\n+ <has_text text="Time range: 3.5-1139.1 seconds (0.1-19 minutes)" />\n+ <has_text text="Mass range: 57.9756-556.8128 m/z" />\n+ <has_text text="Peaks: 380 (about 380 per sample)" />\n+ <has_text text="Peak Groups: 0" />\n+ <has_text text="Sample classes: ." />\n+ </assert_contents>\n+ </output>\n+ </test>\n+ <test>\n+ <param name="input" value="MM14.mzML" ftype="mzxml" />\n+ <param name="methods|method" value="centWave" />\n+ <param name="methods|ppm" value="56" />\n+ <param name="methods|peakwidth" value="5.275,13.5" />\n+ <output name="log">\n+ <assert_contents>\n+ <has_text text="object with 1 samples" />\n+ <has_text text="Time range: 271-307.3 seconds (4.5-5.1 minutes)" />\n+ <has_text text="Mass range: 117.0357-936.7059 m/z" />\n+ <has_text text="Peaks: 222 (about 222 per sample)" />\n+ <has_text text="Peak Groups: 0" />\n+ <has_text text="Sample classes: ." />\n+ </assert_contents>\n+ </output>\n+ </test>\n </tests>\n \n <help><![CDATA[\n@@ -289,7 +366,7 @@\n \n **Example of a metabolomic workflow**\n \n-.. image:: XCMS_Galaxy_workflow.png\n+.. image:: xcms_xcmsset_workflow.png\n \n \n ------\n@@ -306,21 +383,23 @@\n Input files\n -----------\n \n-+---------------------------+------------+\n-| Parameter : num + label | Format |\n-+===========================+============+\n-| 1 : Choose your inputs | zip |\n-+---------------------------+------------+\n++---------------------------+----------------------------------+\n+| Parameter : num + label | Format |\n++===========================+==================================+\n+| OR : Zip file | zip |\n++---------------------------+----------------------------------+\n+| OR : Single file | mzXML, mzML, mzData, netCDF |\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+ | Single file (recommended): You can put a single file as input. That way, you will be able to launch several xcmsSet in parallel and use "xcms.xcmsSet Merger" before "xcms.group"\n+ | Zip file: You can put a zip file containing your inputs: myinputs.zip (containing all your conditions as sub-directories).\n \n-Steps for creating the zip file\n--------------------------------\n+Zip file: Steps for creating the zip file\n+-----------------------------------------\n \n **Step1: Creating your directory and hierarchize the subdirectories**\n \n@@ -478,6 +557,12 @@\n Changelog/News\n --------------\n \n+**Version 2.1.0 - 22/02/2017**\n+\n+- NEW: The W4M tools will be able now to take as input a single file. It will allow to submit in parallel several files and merge them afterward using "xcms.xcmsSet Merger" before "xcms.group".\n+\n+- BUGFIX: the default value of "matchedFilter" -> "Step size to use for profile generation" which was of 0.01 have been changed to fix with the XMCS default values to 0.1\n+\n **Version 2.0.11 - 22/12/2016**\n \n - BUGFIX: propose scanrange for all methods\n' |
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| diff -r 91311aa08cdc -r 15646e937936 destinations_input_type.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/destinations_input_type.py Fri Apr 07 07:35:01 2017 -0400 |
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| @@ -0,0 +1,23 @@ +from galaxy.jobs import JobDestination +import logging +import os + +''' +This file must be placed in lib/galaxy/jobs/rules/ +''' + +def input_type(job): + ''' + This function checks the input file format/extension and decide which destination in the job_conf.xml using + - If it's a zip file, we will launch the job in multi-thread mode (-pe thread 8) + - If it's an individual file (mzxml, mzml, mzdata or netcdf), the job will use for instance (-pe thread 1) + ''' + log = logging.getLogger(__name__) + inp_data = dict( [ ( da.name, da.dataset ) for da in job.input_datasets ] ) + inp_data.update( [ ( da.name, da.dataset ) for da in job.input_library_datasets ] ) + input_extension = inp_data[ "input" ].extension + log.debug("The input extension is %s" % input_extension) + if input_extension in ["mzxml","mzml","mzdata","netcdf"]: + return 'thread1-men_free10' + else: # zip file + return 'thread4-men_free10' |
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| diff -r 91311aa08cdc -r 15646e937936 job_conf.xml.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/job_conf.xml.sample Fri Apr 07 07:35:01 2017 -0400 |
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| @@ -0,0 +1,36 @@ +<?xml version="1.0"?> +<!-- A sample job config that explicitly configures job running the way it is configured by default (if there is no explicit config). --> +<job_conf> + <plugins> + <plugin id="local" type="runner" load="galaxy.jobs.runners.local:LocalJobRunner" workers="4"/> + <plugin id="sge" load="galaxy.jobs.runners.drmaa:DRMAAJobRunner" type="runner"/> + <plugin id="dynamic" type="runner" > + <param id="rules_module">galaxy.jobs.rules</param> + </plugin> + </plugins> + <handlers> + <handler id="main"/> + </handlers> + <destinations default="sge_default"> + <destination id="local" runner="local"/> + <destination id="sge_default" runner="sge"> + <param id="nativeSpecification">-V -w n -q galaxy.q</param> + </destination> + + <destination id="thread1-men_free10" runner="sge"> + <param id="nativeSpecification">-V -w n -q galaxy.q -pe thread 1 -R y -l mem_free=10G </param> + </destination> + <destination id="thread4-men_free10" runner="sge"> + <param id="nativeSpecification">-V -w n -q galaxy.q -pe thread 4 -R y -l mem_free=10G </param> + </destination> + + <destination id="python_destination_input_type" runner="dynamic"> + <param id="type">python</param> + <param id="function">input_type</param> + </destination> + </destinations> + <tools> + <tool destination="python_destination_input_type" id="abims_xcms_xcmsSet" /> + <tool destination="local" id="upload1"/> + </tools> +</job_conf> |
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| diff -r 91311aa08cdc -r 15646e937936 lib.r --- a/lib.r Mon Jan 30 08:52:59 2017 -0500 +++ b/lib.r Fri Apr 07 07:35:01 2017 -0400 |
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| b'@@ -27,168 +27,165 @@\n \n #@author G. Le Corguille\n #This function format ions identifiers\n-formatIonIdentifiers <- function(dataData, numDigitsRT=0, numDigitsMZ=0) {\n- return(make.unique(paste0("M",round(dataData[,"mz"],numDigitsMZ),"T",round(dataData[,"rt"],numDigitsRT))))\n+formatIonIdentifiers <- function(variableMetadata, numDigitsRT=0, numDigitsMZ=0) {\n+ splitDeco = strsplit(as.character(variableMetadata$name),"_")\n+ idsDeco = sapply(splitDeco, function(x) { deco=unlist(x)[2]; if (is.na(deco)) return ("") else return(paste0("_",deco)) })\n+ namecustom = make.unique(paste0("M",round(variableMetadata[,"mz"],numDigitsMZ),"T",round(variableMetadata[,"rt"],numDigitsRT),idsDeco))\n+ variableMetadata=cbind(name=variableMetadata$name, namecustom=namecustom, variableMetadata[,!(colnames(variableMetadata) %in% c("name"))])\n+ return(variableMetadata)\n }\n \n #@author G. Le Corguille\n # value: intensity values to be used into, maxo or intb\n getPeaklistW4M <- function(xset, intval="into",convertRTMinute=F,numDigitsMZ=4,numDigitsRT=0,variableMetadataOutput,dataMatrixOutput) {\n- groups <- xset@groups\n- values <- groupval(xset, "medret", value=intval)\n- \n- # renamming of the column rtmed to rt to fit with camera peaklist function output\n- colnames(groups)[colnames(groups)=="rtmed"] <- "rt"\n- colnames(groups)[colnames(groups)=="mzmed"] <- "mz"\n- \n- ids <- formatIonIdentifiers(groups, numDigitsRT=numDigitsRT, numDigitsMZ=numDigitsMZ)\n- groups = RTSecondToMinute(groups, convertRTMinute)\n+ variableMetadata_dataMatrix = peakTable(xset, method="medret", value=intval)\n+ variableMetadata_dataMatrix = cbind(name=groupnames(xset),variableMetadata_dataMatrix)\n+\n+ dataMatrix = variableMetadata_dataMatrix[,(make.names(colnames(variableMetadata_dataMatrix)) %in% c("name", make.names(sampnames(xset))))]\n \n- rownames(groups) = ids\n- rownames(values) = ids\n+ variableMetadata = variableMetadata_dataMatrix[,!(make.names(colnames(variableMetadata_dataMatrix)) %in% c(make.names(sampnames(xset))))]\n+ variableMetadata = RTSecondToMinute(variableMetadata, convertRTMinute)\n+ variableMetadata = formatIonIdentifiers(variableMetadata, numDigitsRT=numDigitsRT, numDigitsMZ=numDigitsMZ)\n \n- #@TODO: add "name" as the first column name\n- #colnames(groups)[1] = "name"\n- #colnames(values)[1] = "name"\n-\n- write.table(groups, file=variableMetadataOutput,sep="\\t",quote=F,row.names = T,col.names = NA)\n- write.table(values, file=dataMatrixOutput,sep="\\t",quote=F,row.names = T,col.names = NA)\n+ write.table(variableMetadata, file=variableMetadataOutput,sep="\\t",quote=F,row.names=F)\n+ write.table(dataMatrix, file=dataMatrixOutput,sep="\\t",quote=F,row.names=F)\n }\n \n #@author Y. Guitton\n getBPC <- function(file,rtcor=NULL, ...) {\n- object <- xcmsRaw(file)\n- sel <- profRange(object, ...)\n- cbind(if (is.null(rtcor)) object@scantime[sel$scanidx] else rtcor ,xcms:::colMax(object@env$profile[sel$massidx,sel$scanidx,drop=FALSE]))\n- #plotChrom(xcmsRaw(file), base=T)\n+ object <- xcmsRaw(file)\n+ sel <- profRange(object, ...)\n+ cbind(if (is.null(rtcor)) object@scantime[sel$scanidx] else rtcor ,xcms:::colMax(object@env$profile[sel$massidx,sel$scanidx,drop=FALSE]))\n+ #plotChrom(xcmsRaw(file), base=T)\n }\n \n #@author Y. Guitton\n getBPCs <- function (xcmsSet=NULL, pdfname="BPCs.pdf",rt=c("raw","corrected"), scanrange=NULL) {\n- cat("Creating BIC pdf...\\n")\n+ cat("Creating BIC pdf...\\n")\n \n- if (is.null(xcmsSet)) {\n- cat("Enter an xcmsSet \\n")\n- stop()\n- } else {\n- files <- filepaths(xcmsSet)\n- }\n+ if (is.null(xcmsSet)) {\n+ cat("Enter an xcmsSet \\n")\n+ stop()\n+ } else {\n+ files <- filepaths(xcmsSet)\n+ }\n \n- class<-as.vector(levels(xcmsSet@phenoData[,1])) #sometime phenoData have more than 1 column use first as class\n+ phenoDataClass<-as.vector(levels(xcmsSet@phenoData[,1])) #sometime phenoData have more than 1 column use first as class\n \n- classnam'..b'as.matrix(md5sum(files)))\n+}\n+\n+\n+# This function get the raw file path from the arguments\n+getRawfilePathFromArguments <- function(singlefile, zipfile, listArguments) { \n+ if (!is.null(listArguments[["zipfile"]])) zipfile = listArguments[["zipfile"]]\n+ if (!is.null(listArguments[["zipfilePositive"]])) zipfile = listArguments[["zipfilePositive"]]\n+ if (!is.null(listArguments[["zipfileNegative"]])) zipfile = listArguments[["zipfileNegative"]]\n+\n+ if (!is.null(listArguments[["singlefile_galaxyPath"]])) {\n+ singlefile_galaxyPaths = listArguments[["singlefile_galaxyPath"]];\n+ singlefile_sampleNames = listArguments[["singlefile_sampleName"]]\n+ }\n+ if (!is.null(listArguments[["singlefile_galaxyPathPositive"]])) {\n+ singlefile_galaxyPaths = listArguments[["singlefile_galaxyPathPositive"]];\n+ singlefile_sampleNames = listArguments[["singlefile_sampleNamePositive"]]\n+ }\n+ if (!is.null(listArguments[["singlefile_galaxyPathNegative"]])) {\n+ singlefile_galaxyPaths = listArguments[["singlefile_galaxyPathNegative"]];\n+ singlefile_sampleNames = listArguments[["singlefile_sampleNameNegative"]]\n+ }\n+ if (exists("singlefile_galaxyPaths")){\n+ singlefile_galaxyPaths = unlist(strsplit(singlefile_galaxyPaths,","))\n+ singlefile_sampleNames = unlist(strsplit(singlefile_sampleNames,","))\n \n- library(tools)\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+ singlefile[[singlefile_sampleName]] = singlefile_galaxyPath\n+ }\n+ }\n+ for (argument in c("zipfile","zipfilePositive","zipfileNegative","singlefile_galaxyPath","singlefile_sampleName","singlefile_galaxyPathPositive","singlefile_sampleNamePositive","singlefile_galaxyPathNegative","singlefile_sampleNameNegative")) {\n+ listArguments[[argument]]=NULL\n+ }\n+ return(list(zipfile=zipfile, singlefile=singlefile, listArguments=listArguments))\n+}\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+retrieveRawfileInTheWorkingDirectory <- function(singlefile, zipfile) {\n+ if(!is.null(singlefile) && (length("singlefile")>0)) {\n+ for (singlefile_sampleName in names(singlefile)) {\n+ singlefile_galaxyPath = singlefile[[singlefile_sampleName]]\n+ if(!file.exists(singlefile_galaxyPath)){\n+ error_message=paste("Cannot access the sample:",singlefile_sampleName,"located:",singlefile_galaxyPath,". Please, contact your administrator ... if you have one!")\n+ print(error_message); stop(error_message)\n+ }\n \n- #cat("\\n\\n")\n+ file.symlink(singlefile_galaxyPath,singlefile_sampleName)\n+ }\n+ directory = "."\n+\n+ }\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- return(as.matrix(md5sum(files)))\n+ #unzip\n+ suppressWarnings(unzip(zipfile, unzip="unzip"))\n+\n+ #get the directory name\n+ 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+\n+ cat("files_root_directory\\t",directory,"\\n")\n+\n+ }\n+ return (directory)\n }\n' |
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| diff -r 91311aa08cdc -r 15646e937936 macros.xml --- a/macros.xml Mon Jan 30 08:52:59 2017 -0500 +++ b/macros.xml Fri Apr 07 07:35:01 2017 -0400 |
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| @@ -7,6 +7,11 @@ <requirement type="package" version="1.1_4">r-batch</requirement> </requirements> </xml> + <xml name="requirements_light"> + <requirements> + <requirement type="package" version="1.46.0">bioconductor-xcms</requirement> + </requirements> + </xml> <xml name="stdio"> <stdio> <exit_code range="1" level="fatal" /> @@ -20,41 +25,101 @@ <token name="@COMMAND_LOG_EXIT@"> ; return=\$?; - mv log.txt $log; - cat $log; + mv log.txt '$log'; + cat '$log'; sh -c "exit \$return" </token> <!-- zipfile load for planemo test --> - <token name="@COMMAND_ZIPFILE_LOAD@"> - #if $zipfile_load_conditional.zipfile_load_select == "yes": - #if $zipfile_load_conditional.zip_file: - zipfile $zipfile_load_conditional.zip_file + <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="zipfile_load"> - <conditional name="zipfile_load_conditional"> - <param name="zipfile_load_select" type="select" label="Resubmit your zip file" help="Use only if you get a message which say that your original zip file have been deleted on the server." > - <option value="no" >no need</option> - <option value="yes">yes</option> - </param> - <when value="no"> + <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="@COMMAND_PEAKLIST@"> + #if $peaklist.peaklistBool + variableMetadataOutput '$variableMetadata' + dataMatrixOutput '$dataMatrix' + convertRTMinute $peaklist.convertRTMinute + numDigitsMZ $peaklist.numDigitsMZ + numDigitsRT $peaklist.numDigitsRT + intval $peaklist.intval + #end if + </token> + + <xml name="input_peaklist"> + <conditional name="peaklist"> + <param name="peaklistBool" type="boolean" label="Get a Peak List" /> + <when value="true"> + <param name="convertRTMinute" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" label="Convert retention time (seconds) into minutes" help="Convert the columns rtmed, rtmin and rtmax into minutes"/> + <param name="numDigitsMZ" type="integer" value="4" label="Number of decimal places for mass values reported in ions' identifiers." help="A minimum of 4 decimal places is recommended. Useful to avoid duplicates within identifiers" /> + <param name="numDigitsRT" type="integer" value="0" label="Number of decimal places for retention time values reported in ions' identifiers." help="Useful to avoid duplicates within identifiers" /> + <param name="intval" type="select" label="Reported intensity values" help="[intval] See the help section below"> + <option value="into" selected="true">into</option> + <option value="maxo">maxo</option> + <option value="intb">intb</option> + </param> </when> - <when value="yes"> - <param name="zip_file" type="data" format="no_unzip.zip,zip" label="Zip file" /> - </when> + <when value="false" /> </conditional> </xml> - + <xml name="output_peaklist" token_function=""> + <data name="variableMetadata" format="tabular" label="${image.name[:-6]}.@FUNCTION@.variableMetadata.tsv"> + <filter>(peaklist['peaklistBool'])</filter> + </data> + <data name="dataMatrix" format="tabular" label="${image.name[:-6]}.@FUNCTION@.dataMatrix.tsv" > + <filter>(peaklist['peaklistBool'])</filter> + </data> + </xml> <token name="@HELP_AUTHORS@"> .. class:: infomark -**Authors** Colin A. Smith csmith@scripps.edu, Ralf Tautenhahn rtautenh@gmail.com, Steffen Neumann sneumann@ipb-halle.de, Paul Benton hpaul.benton08@imperial.ac.uk and Christopher Conley cjconley@ucdavis.edu +**Authors** Colin A. Smith csmith@scripps.edu, Ralf Tautenhahn rtautenh@gmail.com, Steffen Neumann sneumann@ipb-halle.de, Paul Benton hpaul.benton08@imperial.ac.uk and Christopher Conley cjconley@ucdavis.edu .. class:: infomark |
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| diff -r 91311aa08cdc -r 15646e937936 planemo_test.sh --- a/planemo_test.sh Mon Jan 30 08:52:59 2017 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,31 +0,0 @@ -# Example of planemo command to launch test - - -# -- Use of installed package environments -# after having installing package on a local galaxy instance -source /w/galaxy/dev/shed_tools_tool_dependency_dir/R/3.1.2/iuc/package_r_3_1_2/1ca39eb16186/env.sh -source /w/galaxy/dev/shed_tools_tool_dependency_dir/bioconductor-xcms/1.44.0/lecorguille/package_bioconductor_xcms_1_44_0/0c38f7d43e08/env.sh -planemo test --install_galaxy - -#All 2 test(s) executed passed. -#abims_xcms_xcmsSet[0]: passed -#abims_xcms_xcmsSet[1]: passed - - -# -- 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 - -#All 2 test(s) executed passed. -#abims_xcms_xcmsSet[0]: passed -#abims_xcms_xcmsSet[1]: passed - - -# -- Use of shed_test -planemo shed_test --install_galaxy -t testtoolshed - -#All 2 test(s) executed passed. -#testtoolshed.g2.bx.psu.edu/repos/lecorguille/xcms_group/abims_xcms_xcmsset/2.0.8[0]: passed -#testtoolshed.g2.bx.psu.edu/repos/lecorguille/xcms_group/abims_xcms_xcmsset/2.0.8[1]: passed - |
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| diff -r 91311aa08cdc -r 15646e937936 static/images/XCMS_Galaxy_workflow.png |
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| Binary file static/images/XCMS_Galaxy_workflow.png has changed |
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| diff -r 91311aa08cdc -r 15646e937936 static/images/xcms_xcmsset_workflow.png |
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| Binary file static/images/xcms_xcmsset_workflow.png has changed |
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| diff -r 91311aa08cdc -r 15646e937936 test-data/HU_neg_017.mzXML --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/HU_neg_017.mzXML Fri Apr 07 07:35:01 2017 -0400 |
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| b'@@ -0,0 +1,40676 @@\n+<?xml version="1.0" encoding="ISO-8859-1"?>\n+<mzXML xmlns="http://sashimi.sourceforge.net/schema_revision/mzXML_3.2"\n+ xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"\n+ xsi:schemaLocation="http://sashimi.sourceforge.net/schema_revision/mzXML_3.2 http://sashimi.sourceforge.net/schema_revision/mzXML_3.2/mzXML_idx_3.2.xsd">\n+ <msRun scanCount="2032" startTime="PT0.7297S" endTime="PT1139.62S">\n+ <parentFile fileName="file://Y:/439020_Metabolomic database/Etienne/sacuri-rawToCentroid/HU_neg_017.RAW"\n+ fileType="RAWData"\n+ fileSha1="b632da6cfb9a0c328b718b0018f2765f91f78058"/>\n+ <msInstrument id="IC1">\n+ <msManufacturer category="msManufacturer" value="Thermo Scientific"/>\n+ <msModel category="msModel" value="LTQ Orbitrap Discovery"/>\n+ <msIonisation category="msIonisation" value="electrospray ionization"/>\n+ <msMassAnalyzer category="msMassAnalyzer" value="orbitrap"/>\n+ <msDetector category="msDetector" value="inductive detector"/>\n+ <software type="acquisition" name="Xcalibur" version="2.4 SP1"/>\n+ </msInstrument>\n+ <msInstrument id="IC2">\n+ <msManufacturer category="msManufacturer" value="Thermo Scientific"/>\n+ <msModel category="msModel" value="LTQ Orbitrap Discovery"/>\n+ <msIonisation category="msIonisation" value="electrospray ionization"/>\n+ <msMassAnalyzer category="msMassAnalyzer" value="radial ejection linear ion trap"/>\n+ <msDetector category="msDetector" value="electron multiplier"/>\n+ <software type="acquisition" name="Xcalibur" version="2.4 SP1"/>\n+ </msInstrument>\n+ <dataProcessing centroided="1">\n+ <software type="conversion" name="ProteoWizard" version="2.2.3214"/>\n+ <processingOperation name="Conversion to mzML"/>\n+ <software type="processing" name="ProteoWizard" version="2.2.3214"/>\n+ <comment>Thermo/Xcalibur peak picking</comment>\n+ </dataProcessing>\n+ <scan num="1"\n+ scanEvent="1"\n+ scanType="FULL"\n+ centroided="1"\n+ msLevel="1"\n+ peaksCount="261"\n+ polarity="-"\n+ 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| diff -r 91311aa08cdc -r 15646e937936 test-data/MM14.mzML --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/MM14.mzML Fri Apr 07 07:35:01 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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| diff -r 91311aa08cdc -r 15646e937936 test-data/MM8.mzML --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/MM8.mzML Fri Apr 07 07:35:01 2017 -0400 |
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| b'@@ -0,0 +1,6207 @@\n+<?xml version="1.0" encoding="ISO-8859-1"?>\r\n+<mzML xmlns="http://psi.hupo.org/ms/mzml" xsi:schemaLocation="http://psi.hupo.org/ms/mzml http://psidev.info/files/ms/mzML/xsd/mzML1.1.0.xsd" version="1.1.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">\r\n+<cvList count="2">\r\n+<cv id="MS" fullName="Proteomics Standards Initiative Mass Spectrometry Vocabularies" version="2.26.0" URI="http://psidev.cvs.sourceforge.net/*checkout*/psidev/psi/psi-ms/mzML/controlledVocabulary/psi-ms.obo"/>\r\n+<cv id="UO" fullName="unit" version="1.20" URI="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/unit.obo?revision=1.20"/>\r\n+</cvList>\r\n+<fileDescription>\r\n+<fileContent>\r\n+<cvParam cvRef="MS" accession="MS:1000579" name="MS1 spectrum"/>\r\n+<cvParam cvRef="MS" accession="MS:1000127" name="centroid spectrum"/>\r\n+</fileContent>\r\n+<sourceFileList count="1">\r\n+<sourceFile id="sourceFile" location="Z:/tmp/bruker/MM8_2-F%2c1_01_5950.d" 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|
| b |
| diff -r 91311aa08cdc -r 15646e937936 tool_dependencies.xml --- a/tool_dependencies.xml Mon Jan 30 08:52:59 2017 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,9 +0,0 @@ -<?xml version="1.0"?> -<tool_dependency> - <package name="R" version="3.1.2"> - <repository changeset_revision="4d2fd1413b56" name="package_r_3_1_2" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> - </package> - <package name="bioconductor-xcms" version="1.46.0"> - <repository changeset_revision="779207ed5674" name="package_bioconductor_xcms_1_46_0" owner="lecorguille" toolshed="https://toolshed.g2.bx.psu.edu" /> - </package> -</tool_dependency> |
| b |
| diff -r 91311aa08cdc -r 15646e937936 xcms.r --- a/xcms.r Mon Jan 30 08:52:59 2017 -0500 +++ b/xcms.r Fri Apr 07 07:35:01 2017 -0400 |
| [ |
| b'@@ -15,8 +15,8 @@\n #pkgs=c("xcms","batch")\n pkgs=c("parallel","BiocGenerics", "Biobase", "Rcpp", "mzR", "xcms","snow","batch")\n for(pkg in pkgs) {\n- suppressPackageStartupMessages( stopifnot( library(pkg, quietly=TRUE, logical.return=TRUE, character.only=TRUE)))\n- cat(pkg,"\\t",as.character(packageVersion(pkg)),"\\n",sep="")\n+ suppressPackageStartupMessages( stopifnot( library(pkg, quietly=TRUE, logical.return=TRUE, character.only=TRUE)))\n+ cat(pkg,"\\t",as.character(packageVersion(pkg)),"\\n",sep="")\n }\n source_local <- function(fname){ argv <- commandArgs(trailingOnly = FALSE); base_dir <- dirname(substring(argv[grep("--file=", argv)], 8)); source(paste(base_dir, fname, sep="/")) }\n cat("\\n\\n");\n@@ -38,7 +38,7 @@\n \n #image is an .RData file necessary to use xset variable given by previous tools\n if (!is.null(listArguments[["image"]])){\n- load(listArguments[["image"]]); listArguments[["image"]]=NULL\n+ load(listArguments[["image"]]); listArguments[["image"]]=NULL\n }\n \n #Import the different functions\n@@ -61,110 +61,67 @@\n \n xsetRdataOutput = paste(thefunction,"RData",sep=".")\n if (!is.null(listArguments[["xsetRdataOutput"]])){\n- xsetRdataOutput = listArguments[["xsetRdataOutput"]]; listArguments[["xsetRdataOutput"]]=NULL\n+ xsetRdataOutput = listArguments[["xsetRdataOutput"]]; listArguments[["xsetRdataOutput"]]=NULL\n }\n \n #saving the specific parameters\n rplotspdf = "Rplots.pdf"\n if (!is.null(listArguments[["rplotspdf"]])){\n- rplotspdf = listArguments[["rplotspdf"]]; listArguments[["rplotspdf"]]=NULL\n+ rplotspdf = listArguments[["rplotspdf"]]; listArguments[["rplotspdf"]]=NULL\n }\n sampleMetadataOutput = "sampleMetadata.tsv"\n if (!is.null(listArguments[["sampleMetadataOutput"]])){\n- sampleMetadataOutput = listArguments[["sampleMetadataOutput"]]; listArguments[["sampleMetadataOutput"]]=NULL\n+ sampleMetadataOutput = listArguments[["sampleMetadataOutput"]]; listArguments[["sampleMetadataOutput"]]=NULL\n }\n variableMetadataOutput = "variableMetadata.tsv"\n if (!is.null(listArguments[["variableMetadataOutput"]])){\n- variableMetadataOutput = listArguments[["variableMetadataOutput"]]; listArguments[["variableMetadataOutput"]]=NULL\n+ variableMetadataOutput = listArguments[["variableMetadataOutput"]]; listArguments[["variableMetadataOutput"]]=NULL\n }\n dataMatrixOutput = "dataMatrix.tsv"\n if (!is.null(listArguments[["dataMatrixOutput"]])){\n- dataMatrixOutput = listArguments[["dataMatrixOutput"]]; listArguments[["dataMatrixOutput"]]=NULL\n+ dataMatrixOutput = listArguments[["dataMatrixOutput"]]; listArguments[["dataMatrixOutput"]]=NULL\n }\n if (!is.null(listArguments[["convertRTMinute"]])){\n- convertRTMinute = listArguments[["convertRTMinute"]]; listArguments[["convertRTMinute"]]=NULL\n+ convertRTMinute = listArguments[["convertRTMinute"]]; listArguments[["convertRTMinute"]]=NULL\n }\n if (!is.null(listArguments[["numDigitsMZ"]])){\n- numDigitsMZ = listArguments[["numDigitsMZ"]]; listArguments[["numDigitsMZ"]]=NULL\n+ numDigitsMZ = listArguments[["numDigitsMZ"]]; listArguments[["numDigitsMZ"]]=NULL\n }\n if (!is.null(listArguments[["numDigitsRT"]])){\n numDigitsRT = listArguments[["numDigitsRT"]]; listArguments[["numDigitsRT"]]=NULL\n }\n if (!is.null(listArguments[["intval"]])){\n- intval = listArguments[["intval"]]; listArguments[["intval"]]=NULL\n+ intval = listArguments[["intval"]]; listArguments[["intval"]]=NULL\n }\n \n if (thefunction %in% c("xcmsSet","retcor")) {\n- ticspdf = listArguments[["ticspdf"]]; listArguments[["ticspdf"]]=NULL\n- bicspdf = listArguments[["bicspdf"]]; listArguments[["bicspdf"]]=NULL\n-}\n-\n-#necessary to unzip .zip file uploaded to Galaxy\n-#thanks to .zip file it\'s possible to upload many file as the same time conserving the tree hierarchy of directories\n-\n-\n-if (!is.null(listArguments[["zipfile"]])){\n- zipfile= listArguments[["zipfile"]]; listArguments[["zipfile"]]=NULL\n-}\n-\n-if (!is.null(listArguments[["library"]])){\n- directory=listArguments[["library"]]; listArguments[["library"]]'..b'set), listArguments)\n }\n \n cat("\\n\\n")\n@@ -172,8 +129,6 @@\n \n \n \n-\n-\n # ----- MAIN PROCESSING INFO -----\n cat("\\tMAIN PROCESSING INFO\\n")\n \n@@ -181,12 +136,12 @@\n #Verification of a group step before doing the fillpeaks job.\n \n if (thefunction == "fillPeaks") {\n- res=try(is.null(groupnames(xset)))\n- if (class(res) == "try-error"){\n- error<-geterrmessage()\n- write(error, stderr())\n- stop("You must always do a group step after a retcor. Otherwise it won\'t work for the fillpeaks step")\n- }\n+ res=try(is.null(groupnames(xset)))\n+ if (class(res) == "try-error"){\n+ error<-geterrmessage()\n+ write(error, stderr())\n+ stop("You must always do a group step after a retcor. Otherwise it won\'t work for the fillpeaks step")\n+ }\n \n }\n \n@@ -194,7 +149,7 @@\n #dev.new(file="Rplots.pdf", width=16, height=12)\n pdf(file=rplotspdf, width=16, height=12)\n if (thefunction == "group") {\n- par(mfrow=c(2,2))\n+ par(mfrow=c(2,2))\n }\n #else if (thefunction == "retcor") {\n #try to change the legend display\n@@ -208,6 +163,11 @@\n cat("\\t\\tCOMPUTE\\n")\n xset = do.call(thefunction, listArguments)\n \n+# check if there are no peaks\n+if (nrow(peaks(xset)) == 0) {\n+ stop("No peaks were detected. You should review your settings")\n+}\n+\n \n cat("\\n\\n")\n \n@@ -215,40 +175,38 @@\n \n if (thefunction == "xcmsSet") {\n \n- #transform the files absolute pathways into relative pathways\n- xset@filepaths<-sub(paste(getwd(),"/",sep="") ,"", xset@filepaths)\n+ #transform the files absolute pathways into relative pathways\n+ xset@filepaths<-sub(paste(getwd(),"/",sep="") ,"", xset@filepaths)\n+ if(exists("zipfile") && !is.null(zipfile) && (zipfile!="")) {\n \n- if(exists("zipfile") && (zipfile!="")) {\n+ #Modify the samples names (erase the path)\n+ for(i in 1:length(sampnames(xset))){\n \n- #Modify the samples names (erase the path)\n- for(i in 1:length(sampnames(xset))){\n+ sample_name=unlist(strsplit(sampnames(xset)[i], "/"))\n+ sample_name=sample_name[length(sample_name)]\n+ sample_name= unlist(strsplit(sample_name,"[.]"))[1]\n+ sampnames(xset)[i]=sample_name\n \n- sample_name=unlist(strsplit(sampnames(xset)[i], "/"))\n- sample_name=sample_name[length(sample_name)]\n- sample_name= unlist(strsplit(sample_name,"[.]"))[1]\n- sampnames(xset)[i]=sample_name\n+ }\n \n }\n \n- }\n-\n }\n \n # -- TIC --\n if (thefunction == "xcmsSet") {\n- cat("\\t\\tGET TIC GRAPH\\n")\n- sampleNamesList = getSampleMetadata(xcmsSet=xset, sampleMetadataOutput=sampleMetadataOutput)\n- getTICs(xcmsSet=xset, pdfname=ticspdf,rt="raw")\n- getBPCs(xcmsSet=xset,rt="raw",pdfname=bicspdf)\n+ cat("\\t\\tGET TIC GRAPH\\n")\n+ sampleNamesList = getSampleMetadata(xcmsSet=xset, sampleMetadataOutput=sampleMetadataOutput)\n+ getTICs(xcmsSet=xset, pdfname=ticspdf,rt="raw")\n+ getBPCs(xcmsSet=xset,rt="raw",pdfname=bicspdf)\n } else if (thefunction == "retcor") {\n- cat("\\t\\tGET TIC GRAPH\\n")\n- getTICs(xcmsSet=xset, pdfname=ticspdf,rt="corrected")\n- getBPCs(xcmsSet=xset,rt="corrected",pdfname=bicspdf)\n+ cat("\\t\\tGET TIC GRAPH\\n")\n+ getTICs(xcmsSet=xset, pdfname=ticspdf,rt="corrected")\n+ getBPCs(xcmsSet=xset,rt="corrected",pdfname=bicspdf)\n }\n \n-if (thefunction == "fillPeaks") {\n- cat("\\t\\tGET THE PEAK LIST\\n")\n- getPeaklistW4M(xset,intval,convertRTMinute,numDigitsMZ,numDigitsRT,variableMetadataOutput,dataMatrixOutput)\n+if ((thefunction == "group" || thefunction == "fillPeaks") && exists("intval")) {\n+ getPeaklistW4M(xset,intval,convertRTMinute,numDigitsMZ,numDigitsRT,variableMetadataOutput,dataMatrixOutput)\n }\n \n \n@@ -262,7 +220,7 @@\n \n \n #saving R data in .Rdata file to save the variables used in the present tool\n-objects2save = c("xset","zipfile","listOFlistArguments","md5sumList","sampleNamesList")\n+objects2save = c("xset","zipfile","singlefile","listOFlistArguments","md5sumList","sampleNamesList")\n save(list=objects2save[objects2save %in% ls()], file=xsetRdataOutput)\n \n cat("\\n\\n")\n' |
