| Previous changeset 12:9c037181588e (2017-02-01) Next changeset 14:225cb8347572 (2017-11-29) |
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Commit message:
planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419 |
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modified:
CAMERA.r README.rst abims_CAMERA_annotateDiffreport.xml lib.r macros.xml static/images/annotate_workflow.png test-data/faahKO.xset.group.retcor.group.fillPeaks.annotate.dataMatrix.tsv test-data/faahKO.xset.group.retcor.group.fillPeaks.annotate.variableMetadata.tsv |
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added:
test-data/CASMI_extended_NEG_rules.csv test-data/CASMI_extended_POS_rules.csv test-data/faahKO-single.xset.merged.group.retcor.group.fillpeaks.RData test-data/faahKO.xset.group.retcor.group.fillPeaks.annotate.rules.dataMatrix.tsv test-data/faahKO.xset.group.retcor.group.fillPeaks.annotate.rules.variableMetadata.tsv test-data/ko15.CDF test-data/ko16.CDF test-data/wt15.CDF test-data/wt16.CDF |
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removed:
tool_dependencies.xml |
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| diff -r 9c037181588e -r 1c30ff90f3ae CAMERA.r --- a/CAMERA.r Wed Feb 01 12:24:04 2017 -0500 +++ b/CAMERA.r Fri Apr 07 07:42:18 2017 -0400 |
| [ |
| @@ -11,12 +11,12 @@ #pkgs=c("xcms","batch") pkgs=c("parallel","BiocGenerics", "Biobase", "Rcpp", "mzR", "xcms","snow","igraph","CAMERA","multtest","batch") for(p in pkgs) { - suppressPackageStartupMessages(suppressWarnings(library(p, quietly=TRUE, logical.return=TRUE, character.only=TRUE))) - cat(p,"\t",as.character(packageVersion(p)),"\n",sep="") + suppressPackageStartupMessages(suppressWarnings(library(p, quietly=TRUE, logical.return=TRUE, character.only=TRUE))) + cat(p,"\t",as.character(packageVersion(p)),"\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"); +cat("\n\n"); @@ -34,25 +34,25 @@ #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 + load(listArguments[["image"]]); listArguments[["image"]]=NULL } if (listArguments[["xfunction"]] %in% c("combinexsAnnos")) { - load(listArguments[["image_pos"]]) - xaP=xa - listOFlistArgumentsP=listOFlistArguments - if (exists("xsAnnotate_object")) xaP=xsAnnotate_object - - diffrepP=NULL - if (exists("diffrep")) diffrepP=diffrep + load(listArguments[["image_pos"]]) + xaP=xa + listOFlistArgumentsP=listOFlistArguments + if (exists("xsAnnotate_object")) xaP=xsAnnotate_object + + diffrepP=NULL + if (exists("diffrep")) diffrepP=diffrep - load(listArguments[["image_neg"]]) - xaN=xa - listOFlistArgumentsN=listOFlistArguments - if (exists("xsAnnotate_object")) xaN=xsAnnotate_object + load(listArguments[["image_neg"]]) + xaN=xa + listOFlistArgumentsN=listOFlistArguments + if (exists("xsAnnotate_object")) xaN=xsAnnotate_object - diffrepN=NULL - if (exists("diffrep")) diffrepN=diffrep + diffrepN=NULL + if (exists("diffrep")) diffrepN=diffrep } @@ -73,67 +73,42 @@ xsetRdataOutput = paste(thefunction,"RData",sep=".") if (!is.null(listArguments[["xsetRdataOutput"]])){ - xsetRdataOutput = listArguments[["xsetRdataOutput"]]; listArguments[["xsetRdataOutput"]]=NULL + xsetRdataOutput = listArguments[["xsetRdataOutput"]]; listArguments[["xsetRdataOutput"]]=NULL } rplotspdf = "Rplots.pdf" if (!is.null(listArguments[["rplotspdf"]])){ - rplotspdf = listArguments[["rplotspdf"]]; listArguments[["rplotspdf"]]=NULL + rplotspdf = listArguments[["rplotspdf"]]; listArguments[["rplotspdf"]]=NULL } dataMatrixOutput = "dataMatrix.tsv" if (!is.null(listArguments[["dataMatrixOutput"]])){ - dataMatrixOutput = listArguments[["dataMatrixOutput"]]; listArguments[["dataMatrixOutput"]]=NULL + dataMatrixOutput = listArguments[["dataMatrixOutput"]]; listArguments[["dataMatrixOutput"]]=NULL } variableMetadataOutput = "variableMetadata.tsv" if (!is.null(listArguments[["variableMetadataOutput"]])){ - variableMetadataOutput = listArguments[["variableMetadataOutput"]]; listArguments[["variableMetadataOutput"]]=NULL -} - -if (!is.null(listArguments[["new_file_path"]])){ - new_file_path = listArguments[["new_file_path"]]; listArguments[["new_file_path"]]=NULL + variableMetadataOutput = listArguments[["variableMetadataOutput"]]; listArguments[["variableMetadataOutput"]]=NULL } #Import the different functions source_local("lib.r") -#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 -} - # We unzip automatically the chromatograms from the zip files. if (thefunction %in% c("annotatediff")) { - 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) - } - - #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") - } + if (!exists("zipfile")) zipfile=NULL + if (!exists("singlefile")) singlefile=NULL + rawFilePath = getRawfilePathFromArguments(singlefile, zipfile, listArguments) + zipfile = rawFilePath$zipfile + singlefile = rawFilePath$singlefile + listArguments = rawFilePath$listArguments + directory = retrieveRawfileInTheWorkingDirectory(singlefile, zipfile) } - #addition of xset object to the list of arguments in the first position if (exists("xset") != 0){ - listArguments=append(list(xset), listArguments) + listArguments=append(list(xset), listArguments) } cat("\n\n") @@ -149,25 +124,32 @@ if (thefunction %in% c("annotatediff")) { - results_list=annotatediff(xset=xset,listArguments=listArguments,variableMetadataOutput=variableMetadataOutput,dataMatrixOutput=dataMatrixOutput,new_file_path=new_file_path) - xa=results_list[["xa"]] - diffrep=results_list[["diffrep"]] - variableMetadata=results_list[["variableMetadata"]] + results_list=annotatediff(xset=xset,listArguments=listArguments,variableMetadataOutput=variableMetadataOutput,dataMatrixOutput=dataMatrixOutput) + xa=results_list[["xa"]] + diffrep=results_list[["diffrep"]] + variableMetadata=results_list[["variableMetadata"]] - cat("\n\n") - cat("\tXSET OBJECT INFO\n") - print(xa) + cat("\n\n") + cat("\tXSET OBJECT INFO\n") + print(xa) } if (thefunction %in% c("combinexsAnnos")) { - cAnnot=combinexsAnnos_function(xaP=xaP,xaN=xaN,listOFlistArgumentsP=listOFlistArgumentsP,listOFlistArgumentsN=listOFlistArgumentsN,diffrepP=diffrepP,diffrepN=diffrepN,convert_param=listArguments[["convert_param"]],pos=listArguments[["pos"]],tol=listArguments[["tol"]],ruleset=listArguments[["ruleset"]],keep_meta=listArguments[["keep_meta"]],variableMetadataOutput=variableMetadataOutput) + cAnnot=combinexsAnnos_function( + xaP=xaP,xaN=xaN, + listOFlistArgumentsP=listOFlistArgumentsP,listOFlistArgumentsN=listOFlistArgumentsN, + diffrepP=diffrepP,diffrepN=diffrepN, + pos=listArguments[["pos"]],tol=listArguments[["tol"]],ruleset=listArguments[["ruleset"]],keep_meta=listArguments[["keep_meta"]], + convertRTMinute=listArguments[["convertRTMinute"]], numDigitsMZ=listArguments[["numDigitsMZ"]], numDigitsRT=listArguments[["numDigitsRT"]], + variableMetadataOutput=variableMetadataOutput + ) } dev.off() #saving R data in .Rdata file to save the variables used in the present tool -objects2save = c("xa","variableMetadata","diffrep","cAnnot","listOFlistArguments","zipfile") +objects2save = c("xa","variableMetadata","diffrep","cAnnot","listOFlistArguments","zipfile","singlefile") save(list=objects2save[objects2save %in% ls()], file=xsetRdataOutput) cat("\n\n") |
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| diff -r 9c037181588e -r 1c30ff90f3ae README.rst --- a/README.rst Wed Feb 01 12:24:04 2017 -0500 +++ b/README.rst Fri Apr 07 07:42:18 2017 -0400 |
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| @@ -2,6 +2,21 @@ Changelog/News -------------- +**Version 2.2.0 - 03/02/2017** + +- BUGFIX: the diffreport ids didn't convert the rt in minute as the other export + +- UPDATE: the settings (digits, convertion in minutes) of the identifiants will no longer modify the native one. Because we want to be conservative and because it can be dangerous for the data integrity during a futur merge of the table, we decide to put those customization in a new column namecustom within the variableMetadata. + +- IMPROVEMENT: add some sections within the form to separate the different parts of the process + +- IMPROVEMENT: add the possibility to use defined ruleset + +- IMPROVEMENT: add the possibility to set the MZ digit within the identifiants + +- IMPROVEMENT: CAMERA.annotate is now compatible with merged individual data from xcms.xcmsSet + + **Version 2.1.5 - 21/04/2016** - UPGRADE: upgrate the CAMERA version from 1.22.0 to 1.26.0 @@ -22,26 +37,15 @@ - UPDATE: refactoring of internal management of inputs/outputs -VERSION 2.1.0 - 09/10/2015** +**VERSION 2.1.0 - 09/10/2015** - BUGFIX: There was a bug with the CAMERA.annotate (generating a bad dataMatrix (intensities which don't match with the metabolites)) -VERSION 2.1.0 - 07/06/2015** +**VERSION 2.1.0 - 07/06/2015** - IMPROVEMENT: new datatype/dataset formats (rdata.camera.positive, rdata.camera.negative, rdata.camera.quick ...) will facilitate the sequence of tools and so avoid incompatibility errors. - IMPROVEMENT: parameter labels have changed to facilitate their reading. - UPDATE: merged with annotateDiffreport. Some parameters are dedicated to experiences with several conditions - - - -Test Status ------------ - -Planemo test using conda: passed - -Planemo test using source env.sh: passed - -Planemo shed_test : passed |
| b |
| diff -r 9c037181588e -r 1c30ff90f3ae abims_CAMERA_annotateDiffreport.xml --- a/abims_CAMERA_annotateDiffreport.xml Wed Feb 01 12:24:04 2017 -0500 +++ b/abims_CAMERA_annotateDiffreport.xml Fri Apr 07 07:42:18 2017 -0400 |
| [ |
| b'@@ -1,7 +1,7 @@\n-<tool id="abims_CAMERA_annotateDiffreport" name="CAMERA.annotate" version="2.1.5">\n+<tool id="abims_CAMERA_annotateDiffreport" name="CAMERA.annotate" version="2.2.0">\n \n <description>CAMERA annotate function. Returns annotation results (isotope peaks, adducts and fragments) and a diffreport if more than one condition.</description>\n- \n+\n <macros>\n <import>macros.xml</import>\n </macros>\n@@ -11,213 +11,225 @@\n \n <command><![CDATA[\n @COMMAND_CAMERA_SCRIPT@\n- xfunction annotatediff \n- image $image\n+ xfunction annotatediff\n+ image \'$image\'\n \n- variableMetadataOutput $variableMetadata\n- dataMatrixOutput $datamatrix\n- xsetRdataOutput $rdata\n-\n- convert_param $convert_param num_digits $num_digits \n nSlaves \\${GALAXY_SLOTS:-1}\n- sigma $sigma perfwhm $perfwhm \n- maxcharge $maxcharge maxiso $maxiso minfrac $minfrac\n- ppm $ppm mzabs $mzabs intval $intval \n- max_peaks $max_peaks\n+\n+ ## output\n+ variableMetadataOutput \'$variableMetadata\'\n+ dataMatrixOutput \'$datamatrix\'\n+\n+ ## groupFWHM\n+ sigma $groupfwhm.sigma\n+ perfwhm $groupfwhm.perfwhm\n+\n+ ## findGeneral\n+ ppm $findgeneral.ppm\n+ mzabs $findgeneral.mzabs\n+\n+ ## findIsotopes\n+ maxcharge $findisotopes.maxcharge\n+ maxiso $findisotopes.maxiso\n+ minfrac $findisotopes.minfrac\n+\n quick $quick_block.quick\n- #if $quick_block.quick == "FALSE"\n- polarity $quick_block.polarity\n- cor_eic_th $quick_block.cor_eic_th\n- graphMethod $quick_block.graphMethod \n- pval $quick_block.pval \n- calcCiS $quick_block.calcCiS\n- calcIso $quick_block.calcIso\n- calcCaS $quick_block.calcCaS\n- multiplier $quick_block.multiplier\n+ #if $quick_block.quick == "FALSE":\n+ xsetRdataOutput \'$rdata_quick_false\'\n+\n+ ## groupcorr\n+ cor_eic_th $quick_block.groupcorr.cor_eic_th\n+ graphMethod $quick_block.groupcorr.graphMethod\n+ pval $quick_block.groupcorr.pval\n+ calcCiS $quick_block.groupcorr.calcCiS\n+ calcIso $quick_block.groupcorr.calcIso\n+ calcCaS $quick_block.groupcorr.calcCaS\n+\n+ ## findadducts\n+ polarity $quick_block.findadducts.polarity\n+ max_peaks $quick_block.findadducts.max_peaks\n+ #if $quick_block.findadducts.rules_block.rules_select == "FALSE":\n+ multiplier $quick_block.findadducts.rules_block.multiplier\n+ #else\n+ rules $quick_block.findadducts.rules_block.rules\n+ #end if\n+ #else\n+ xsetRdataOutput \'$rdata_quick_true\'\n #end if\n \n- #if $options.option == "show":\n+ #if $diffreport.options.option == "show":\n+ ## diffreport\n runDiffreport TRUE\n- eicmax $options.eicmax\n- eicwidth $options.eicwidth\n- value $options.value\n- sortpval $options.sortpval \n- h $options.h\n- w $options.w\n- mzdec $options.mzdec\n- new_file_path ${__new_file_path__}/primary_${output_diffreport.id}_\n+ eicmax $diffreport.options.eicmax\n+ eicwidth $diffreport.options.eicwidth\n+ value $diffreport.options.value\n+ sortpval $diffreport.options.sortpval\n+ h $diffreport.options.h\n+ w $diffreport.options.w\n+ mzdec $diffreport.options.mzdec\n #end if\n- \n- @COMMAND_ZIPFILE_LOAD@\n+\n+ @COMMAND_PEAKLIST@\n+\n+ @COMMAND_FILE_LOAD@\n \n ]]></command>\n \n <inputs>\n- \n- \n+\n+\n <param name="image" type="data" label="RData file" format="rdata.xcms.fillpeaks,rdata" help="output file from another function xcms (fillPeaks)" />\n \n- <param name="convert_param" type="boolean" che'..b'ive |\n+|CAMERA_combinexsAnnot |xset.annotate.Rdata | rdata.camera.positive or rdata.camera.negative |\n +---------------------------+---------------------------------------+------------------------------------------------+\n |Determine Vdk or Lowess |xset.annotate.dataMatrix.tsv | Tabular |\n +---------------------------+---------------------------------------+------------------------------------------------+\n@@ -303,6 +315,22 @@\n +---------------------------+---------------------------+\n \n \n+[Optional] User defined ruleset:\n+--------------------------------\n+\n+Example:\n+\n+ | "name","nmol","charge","massdiff","oidscore","quasi","ips"\n+ | "[M-H]-",1,-1,-1.007276,1,1,1\n+ | "[M-2H]2-",1,-2,-2.014552,2,0,1\n+ | "[M-3H]3-",1,-3,-3.021828,3,0,1\n+ | "[M-2H+Na]-",1,-1,20.974666,4,0,0.25\n+ | "[M-H+Cl]2-",1,-2,33.962126,5,0,1\n+ | "[M-2H+K]-",1,-1,36.948606,6,0,0.25\n+ | "[M+Cl]-",1,-1,34.969402,7,1,1\n+ | "[M+2Cl]2-",1,-2,69.938804,8,0,1\n+ | "[2M-H]-",2,-1,-1.007276,1,0,0.5\n+\n ----------\n Parameters\n ----------\n@@ -328,7 +356,7 @@\n xset.annotate.dataMatrix.tsv\n \n | A tabular file which represents for each metabolite (row), the value of the intensity in each sample (column).\n- \n+\n xset.annotate.zip\n \n | It contains filebase_eic, filebase_box and filebase.tsv for one conditon vs another (Anova analysis).\n@@ -336,10 +364,10 @@\n xset.annotate.Rdata rdata.camera.quick or rdata.camera.positive or rdata.camera.negative\n \n | Rdata file, that be used outside Galaxy in R.\n- \n+\n ------\n \n-.. class:: infomark \n+.. class:: infomark\n \n The output **"xset.annotate.dataMatrix.tsv"** is a tabular file. You can continue your analysis using it in the following tools of the workflow:\n \n@@ -349,7 +377,7 @@\n | PCA (Statistical analysis)\n | Hierarchical Clustering (Statistical analysis)\n \n- \n+\n ---------------------------------------------------\n \n ---------------\n@@ -377,7 +405,7 @@\n | eicmax -> **200**\n | eicwidth -> **200 (default)**\n \n- \n+\n \n Output files\n ------------\n@@ -386,7 +414,7 @@\n \n .. image:: annotatediffreport_dataMatrix.png\n \n-**Example of a part of xset.annotate.variableMetadata.tsv output** \n+**Example of a part of xset.annotate.variableMetadata.tsv output**\n \n .. image:: annotatediffreport_variableMetadata.png\n \n@@ -396,9 +424,24 @@\n Changelog/News\n --------------\n \n+**Version 2.2.0 - 28/03/2017**\n+\n+- BUGFIX: the diffreport ids didn\'t convert the rt in minute as the other export\n+\n+- UPDATE: the settings (digits, convertion in minutes) of the identifiants will no longer modify the native one. Because we want to be conservative and because it can be dangerous for the data integrity during a futur merge of the table, we decide to put those customization in a new column namecustom within the variableMetadata.\n+\n+- IMPROVEMENT: add some sections within to separate the different parts of the process\n+\n+- IMPROVEMENT: add the possibility to use defined ruleset\n+\n+- IMPROVEMENT: add the possibility to set the MZ digit within the identifiants\n+\n+- IMPROVEMENT: CAMERA.annotate is now compatible with merged individual data from xcms.xcmsSet\n+\n+\n **Version 2.1.5 - 21/04/2016**\n \n-- UPGRADE: upgrate the CAMERA version from 1.22.0 to 1.26.0\n+- UPGRADE: upgrade the CAMERA version from 1.22.0 to 1.26.0\n \n \n **Version 2.1.4 - 18/04/2016**\n@@ -417,12 +460,12 @@\n - UPDATE: refactoring of internal management of inputs/outputs\n \n \n-VERSION 2.1.0 - 09/10/2015**\n+**VERSION 2.1.0 - 09/10/2015**\n \n - BUGFIX: There was a bug with the CAMERA.annotate (generating a bad dataMatrix (intensities which don\'t match with the metabolites))\n \n \n-VERSION 2.1.0 - 07/06/2015**\n+**VERSION 2.1.0 - 07/06/2015**\n \n - IMPROVEMENT: new datatype/dataset formats (rdata.camera.positive, rdata.camera.negative, rdata.camera.quick ...) will facilitate the sequence of tools and so avoid incompatibility errors.\n \n@@ -437,5 +480,3 @@\n \n \n </tool>\n- \n- \n' |
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| diff -r 9c037181588e -r 1c30ff90f3ae lib.r --- a/lib.r Wed Feb 01 12:24:04 2017 -0500 +++ b/lib.r Fri Apr 07 07:42:18 2017 -0400 |
| [ |
| b'@@ -1,188 +1,304 @@\n-# lib.r version="2.2.1"\n+# lib.r\n+\n+#@author G. Le Corguille\n+#The function create a pdf from the different png generated by diffreport\n+diffreport_png2pdf <- function(filebase) {\n+ dir.create("pdf")\n \n-#The function create a pdf from the different png generated by diffreport\n-diffreport_png2pdf <- function(filebase, new_file_path) {\n+ pdfEicOutput = paste0("pdf/",filebase,"-eic_pdf.pdf")\n+ pdfBoxOutput = paste0("pdf/",filebase,"-box_pdf.pdf")\n+\n+ system(paste0("gm convert ",filebase,"_eic/*.png ",pdfEicOutput))\n+ system(paste0("gm convert ",filebase,"_box/*.png ",pdfBoxOutput))\n+\n+}\n \n- pdfEicOutput = paste(new_file_path,filebase,"-eic_visible_pdf",sep="")\n- pdfBoxOutput = paste(new_file_path,filebase,"-box_visible_pdf",sep="")\n+#@author G. Le Corguille\n+#This function convert if it is required the Retention Time in minutes\n+RTSecondToMinute <- function(variableMetadata, convertRTMinute) {\n+ if (convertRTMinute){\n+ #converting the retention times (seconds) into minutes\n+ print("converting the retention times into minutes in the variableMetadata")\n+ variableMetadata[,"rt"]=variableMetadata[,"rt"]/60\n+ variableMetadata[,"rtmin"]=variableMetadata[,"rtmin"]/60\n+ variableMetadata[,"rtmax"]=variableMetadata[,"rtmax"]/60\n+ }\n+ return (variableMetadata)\n+}\n \n- system(paste("gm convert ",filebase,"_eic/*.png ",filebase,"_eic.pdf",sep=""))\n- system(paste("gm convert ",filebase,"_box/*.png ",filebase,"_box.pdf",sep=""))\n-\n- file.copy(paste(filebase,"_eic.pdf",sep=""), pdfEicOutput)\n- file.copy(paste(filebase,"_box.pdf",sep=""), pdfBoxOutput)\n+#@author G. Le Corguille\n+#This function format ions identifiers\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 #The function annotateDiffreport without the corr function which bugs\n-annotatediff <- function(xset=xset, listArguments=listArguments, variableMetadataOutput="variableMetadata.tsv", dataMatrixOutput="dataMatrix.tsv",new_file_path=NULL) {\n- # Resolve the bug with x11, with the function png\n- options(bitmapType=\'cairo\')\n-\n- #Check if the fillpeaks step has been done previously, if it hasn\'t, there is an error message and the execution is stopped.\n- res=try(is.null(xset@filled))\n-\n- # ------ annot -------\n- listArguments[["calcCiS"]]=as.logical(listArguments[["calcCiS"]])\n- listArguments[["calcIso"]]=as.logical(listArguments[["calcIso"]])\n- listArguments[["calcCaS"]]=as.logical(listArguments[["calcCaS"]])\n+annotatediff <- function(xset=xset, listArguments=listArguments, variableMetadataOutput="variableMetadata.tsv", dataMatrixOutput="dataMatrix.tsv") {\n+ # Resolve the bug with x11, with the function png\n+ options(bitmapType=\'cairo\')\n \n- #graphMethod parameter bugs where this parameter is not defined in quick=true\n- if(listArguments[["quick"]]==TRUE) {\n- xa= annotate(object=xset,nSlaves=1,sigma=listArguments[["sigma"]],perfwhm=listArguments[["perfwhm"]],maxcharge=listArguments[["maxcharge"]],maxiso=listArguments[["maxiso"]],minfrac=listArguments[["minfrac"]],ppm=listArguments[["ppm"]],mzabs=listArguments[["mzabs"]],quick=listArguments[["quick"]],polarity=listArguments[["polarity"]],max_peaks=listArguments[["max_peaks"]],intval=listArguments[["intval"]])\n- }\n- else {\n- xa= annotate(object=xset,nSlaves=1,sigma=listArguments[["sigma"]],perfwhm=listArguments[["perfwhm"]],graphMethod=listArguments[["graphMethod"]],cor_eic_th=listArguments[["cor_'..b'sep="\\t", quote=FALSE, row.names=FALSE, file=variableMetadataOutput)\n+ return(variableMetadata);\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+ 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+ 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+ #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' |
| b |
| diff -r 9c037181588e -r 1c30ff90f3ae macros.xml --- a/macros.xml Wed Feb 01 12:24:04 2017 -0500 +++ b/macros.xml Fri Apr 07 07:42:18 2017 -0400 |
| [ |
| b'@@ -2,12 +2,11 @@\n <macros>\n <xml name="requirements">\n <requirements>\n-\t <requirement type="package" version="0.4_1">r-snow</requirement>\n+ <requirement type="package" version="0.4_1">r-snow</requirement>\n <requirement type="package" version="1.26.0">bioconductor-camera</requirement>\n <requirement type="package" version="2.26.0">bioconductor-multtest</requirement>\n-\t <requirement type="package" version="1.1_4">r-batch</requirement>\n- <requirement type="package" version="1.6.27">libpng</requirement>\n- <requirement type="package" version="1.3.20">graphicsmagick</requirement>\n+ <requirement type="package" version="1.1_4">r-batch</requirement>\n+ <requirement type="package" version="1.3.23">graphicsmagick</requirement>\n </requirements>\n </xml>\n <xml name="stdio">\n@@ -19,33 +18,137 @@\n <token name="@COMMAND_CAMERA_SCRIPT@">\n LANG=C Rscript $__tool_directory__/CAMERA.r\n </token>\n- \n- <!-- zipfile load for planemo test -->\n- <token name="@COMMAND_ZIPFILE_LOAD@">\n- #if $zipfile_load_conditional.zipfile_load_select == "yes":\n- #if $zipfile_load_conditional.zip_file:\n- zipfile $zipfile_load_conditional.zip_file\n+\n+ <!-- raw file load for planemo test -->\n+ <token name="@COMMAND_FILE_LOAD@">\n+ #if $file_load_section.file_load_conditional.file_load_select == "yes":\n+ #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"):\n+ #set singlefile_galaxyPath = \',\'.join( [ str( $single_file ) for $single_file in $file_load_section.file_load_conditional.input ] )\n+ #set singlefile_sampleName = \',\'.join( [ str( $single_file.name ) for $single_file in $file_load_section.file_load_conditional.input ] )\n+ singlefile_galaxyPath \'$singlefile_galaxyPath\' singlefile_sampleName \'$singlefile_sampleName\'\n+ #else\n+ zipfile \'$file_load_section.file_load_conditional.input\'\n #end if\n- #end if \n+ #end if\n+ </token>\n+\n+ <xml name="input_file_load">\n+ <section name="file_load_section" title="Resubmit your raw dataset or your zip file">\n+ <conditional name="file_load_conditional">\n+ <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." >\n+ <option value="no" >no need</option>\n+ <option value="yes" >yes</option>\n+ </param>\n+ <when value="no">\n+ </when>\n+ <when value="yes">\n+ <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." />\n+ </when>\n+ </conditional>\n+ </section>\n+ </xml>\n+\n+ <xml name="test_file_load_zip">\n+ <section name="file_load_section">\n+ <conditional name="file_load_conditional">\n+ <param name="file_load_select" value="yes" />\n+ <param name="input" value="faahKO_reduce.zip" ftype="zip" />\n+ </conditional>\n+ </section>\n+ </xml>\n+\n+ <xml name="test_file_load_single">\n+ <section name="file_load_section">\n+ <conditional name="file_load_conditional">\n+ <param name="file_load_select" value="yes" />\n+ <param name="input'..b'ion>\n+\n+ <xml name="input_peaklist">\n+ <section name="export" title="Export options">\n+ <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"/>\n+ <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" />\n+ <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" />\n+ <param name="intval" type="select" label="General used intensity value" help="[intval] See the help section below">\n+ <option value="into" selected="true">into</option>\n+ <option value="maxo" >maxo</option>\n+ <option value="intb">intb</option>\n </param>\n- <when value="no">\n- </when>\n- <when value="yes">\n- <param name="zip_file" type="data" format="no_unzip.zip,zip" label="Zip file" />\n- </when>\n+ </section>\n+ </xml>\n+\n+ <xml name="test_peaklist">\n+ <section name="export">\n+ <param name="convertRTMinute" value="True"/>\n+ <param name="numDigitsMZ" value="4" />\n+ <param name="numDigitsRT" value="1" />\n+ <param name="intval" value="into"/>\n+ </section>\n+ </xml>\n+\n+ <!-- annotate_diffreport <test> commun part -->\n+ <xml name="test_annotate_diffreport">\n+ <section name="groupfwhm">\n+ <param name="sigma" value="6"/>\n+ <param name="perfwhm" value="0.6"/>\n+ </section>\n+ <section name="findisotopes">\n+ <param name="maxcharge" value="3"/>\n+ <param name="maxiso" value="4"/>\n+ <param name="minfrac" value="0.5"/>\n+ </section>\n+ <section name="findgeneral">\n+ <param name="ppm" value="5"/>\n+ <param name="mzabs" value="0.015"/>\n+ <param name="max_peaks" value="100"/>\n+ </section>\n+ <section name="diffreport">\n+ <conditional name="options">\n+ <param name="option" value="show"/>\n+ <param name="eicmax" value="200"/>\n+ <param name="eicwidth" value="200"/>\n+ <param name="value" value="into"/>\n+ <param name="h" value="480"/>\n+ <param name="w" value="640"/>\n+ <param name="mzdec" value="2"/>\n+ <param name="sortpval" value="False"/>\n+ </conditional>\n+ </section>\n+ <expand macro="test_peaklist"/>\n+ </xml>\n+\n+ <xml name="test_annotate_quick_false">\n+ <param name="quick" value="FALSE"/>\n+ <section name="groupcorr">\n+ <param name="cor_eic_th" value="0.75"/>\n+ <param name="graphMethod" value="hcs"/>\n+ <param name="pval" value="0.05"/>\n+ <param name="calcCiS" value="True"/>\n+ <param name="calcIso" value="False"/>\n+ <param name="calcCaS" value="False"/>\n+ </section>\n+ </xml>\n+\n+ <xml name="test_annotate_quick_true">\n+ <conditional name="quick_block">\n+ <param name="quick" value="TRUE"/>\n </conditional>\n </xml>\n- \n+\n <token name="@HELP_AUTHORS@">\n .. class:: infomark\n \n-**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 \n+**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\n \n .. class:: infomark\n \n' |
| b |
| diff -r 9c037181588e -r 1c30ff90f3ae static/images/annotate_workflow.png |
| b |
| Binary file static/images/annotate_workflow.png has changed |
| b |
| diff -r 9c037181588e -r 1c30ff90f3ae test-data/CASMI_extended_NEG_rules.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/CASMI_extended_NEG_rules.csv Fri Apr 07 07:42:18 2017 -0400 |
| [ |
| @@ -0,0 +1,111 @@ +"name","nmol","charge","massdiff","oidscore","quasi","ips" +"[M-H]-",1,-1,-1.007276,1,1,1 +"[M-2H]2-",1,-2,-2.014552,2,0,1 +"[M-3H]3-",1,-3,-3.021828,3,0,1 +"[M-2H+Na]-",1,-1,20.974666,4,0,0.25 +"[M-H+Cl]2-",1,-2,33.962126,5,0,1 +"[M-2H+K]-",1,-1,36.948606,6,0,0.25 +"[M+Cl]-",1,-1,34.969402,7,1,1 +"[M+2Cl]2-",1,-2,69.938804,8,0,1 +"[2M-H]-",2,-1,-1.007276,1,0,0.5 +"[2M-2H]2-",2,-2,-2.014552,2,0,0.5 +"[2M-3H]3-",2,-3,-3.021828,3,0,0.5 +"[2M-2H+Na]-",2,-1,20.974666,4,0,0.25 +"[2M-H+Cl]2-",2,-2,33.962126,5,0,0.5 +"[2M-2H+K]-",2,-1,36.948606,6,0,0.25 +"[2M+Cl]-",2,-1,34.969402,7,0,0.5 +"[2M+2Cl]2-",2,-2,69.938804,8,0,0.5 +"[3M-H]-",3,-1,-1.007276,1,0,0.5 +"[3M-2H]2-",3,-2,-2.014552,2,0,0.5 +"[3M-3H]3-",3,-3,-3.021828,3,0,0.5 +"[3M-2H+Na]-",3,-1,20.974666,4,0,0.25 +"[3M-H+Cl]2-",3,-2,33.962126,5,0,0.5 +"[3M-2H+K]-",3,-1,36.948606,6,0,0.25 +"[3M+Cl]-",3,-1,34.969402,7,0,0.5 +"[3M+2Cl]2-",3,-2,69.938804,8,0,0.5 +"[M+Cl+NaCOOH]-",1,-1,102.956842,9,0,0.5 +"[M-H+NaCOOH]-",1,-1,66.980164,10,0,0.5 +"[M+Cl+HCOOH]-",1,-1,80.974872,11,0,0.5 +"[M+HCOO]-",1,-1,44.99765,12,0,1 +"[M+Cl+CF3COOH]-",1,-1,148.962402,13,0,0.5 +"[M-H+CF3COOH]-",1,-1,112.985724,14,0,0.5 +"[M+Cl+NH3]-",1,-1,51.995952,15,0,0.5 +"[M-H+NH3]-",1,-1,16.019274,16,0,0.5 +"[M-H-CH4]-",1,-1,-17.038576,17,0,0.25 +"[M-H-CO]-",1,-1,-29.002176,18,0,0.25 +"[M-H-C2H2O2]-",1,-1,-47.012746,19,0,0.25 +"[M-H-C3H2O3]-",1,-1,-87.007666,20,0,0.25 +"[M-H-C5H8O4]-",1,-1,-133.049536,21,0,0.25 +"[M-H-C6H10O4]-",1,-1,-147.065186,22,0,0.25 +"[M-H-C6H10O5]-",1,-1,-163.060096,23,0,0.25 +"[M-H-C6H8O6]-",1,-1,-177.039366,24,0,0.25 +"[M-H-H2]-",1,-1,-3.02292607,25,0,0.25 +"[M-H-CH2]-",1,-1,-15.02292607,26,0,0.25 +"[M-H-CH3]-",1,-1,-16.030751105,27,0,0.25 +"[M-H-NH3]-",1,-1,-18.033826,28,0,0.25 +"[M-H-H2O]-",1,-1,-19.0178407,29,0,0.25 +"[M-H-H4O2]-",1,-1,-37.0284054,30,0,0.25 +"[M-H-HF]-",1,-1,-21.013504255,31,0,0.25 +"[M-H-C2H2]-",1,-1,-27.02292607,32,0,0.25 +"[M-H-C2H3]-",1,-1,-28.030751105,33,0,0.25 +"[M-H-HCN]-",1,-1,-28.018175037,34,0,0.25 +"[M-H-C2H4]-",1,-1,-29.03857614,35,0,0.25 +"[M-H-C2H6]-",1,-1,-31.05422621,36,0,0.25 +"[M-H-CH2O]-",1,-1,-31.0178407,37,0,0.25 +"[M-H-CH5N]-",1,-1,-32.049475177,38,0,0.25 +"[M-H-CH4O]-",1,-1,-33.03349077,39,0,0.25 +"[M-H-H2S]-",1,-1,-34.99499677,40,0,0.25 +"[M-H-HCl]-",1,-1,-36.983953755,41,0,0.25 +"[M-H-C3H2]-",1,-1,-39.02292607,42,0,0.25 +"[M-H-C2N]-",1,-1,-39.010350002,43,0,0.25 +"[M-H-F2]-",1,-1,-39.00408244,44,0,0.25 +"[M-H-C3H3]-",1,-1,-40.030751105,45,0,0.25 +"[M-H-HC2N]-",1,-1,-40.018175037,46,0,0.25 +"[M-H-C3H4]-",1,-1,-41.03857614,47,0,0.25 +"[M-H-C3H6]-",1,-1,-43.05422621,48,0,0.25 +"[M-H-C2H2O]-",1,-1,-43.0178407,49,0,0.25 +"[M-H-C3H6]-",1,-1,-43.05422621,50,0,0.25 +"[M-H-NCO]-",1,-1,-43.005264632,51,0,0.25 +"[M-H-CN2H2]-",1,-1,-43.029074074,52,0,0.25 +"[M-H-HCNO]-",1,-1,-44.013089667,53,0,0.25 +"[M-H-C2H4O]-",1,-1,-45.03349077,54,0,0.25 +"[M-H-CO2]-",1,-1,-44.99710526,55,0,0.25 +"[M-H-N2O]-",1,-1,-45.008338634,56,0,0.25 +"[M-H-CONH2]-",1,-1,-45.020914702,57,0,0.25 +"[M-H-NC2H7]-",1,-1,-46.065125247,58,0,0.25 +"[M-H-C2H6O]-",1,-1,-47.04914084,59,0,0.25 +"[M-H-NO2]-",1,-1,-47.000179262,60,0,0.25 +"[M-H-CH4S]-",1,-1,-49.01064684,61,0,0.25 +"[M-H-C4H4]-",1,-1,-53.03857614,62,0,0.25 +"[M-H-C2N2]-",1,-1,-53.013424004,63,0,0.25 +"[M-H-C4H6]-",1,-1,-55.05422621,64,0,0.25 +"[M-H-C4H8]-",1,-1,-57.06987628,65,0,0.25 +"[M-H-C3H6O]-",1,-1,-59.04914084,66,0,0.25 +"[M-H-C4H10]-",1,-1,-59.08552635,67,0,0.25 +"[M-H-C2H5NO]-",1,-1,-60.044389807,68,0,0.25 +"[M-H-C3H8O]-",1,-1,-61.06479091,69,0,0.25 +"[M-H-C2H4O2]-",1,-1,-61.0284054,70,0,0.25 +"[M-H-C2H5Cl]-",1,-1,-65.015253895,71,0,0.25 +"[M-H-C5H4]-",1,-1,-65.03857614,72,0,0.25 +"[M-H-SO2]-",1,-1,-64.96917596,73,0,0.25 +"[M-H-C5H8]-",1,-1,-69.06987628,74,0,0.25 +"[M-H-C5H12]-",1,-1,-73.10117642,75,0,0.25 +"[M-H-C3H6O2]-",1,-1,-75.04405547,76,0,0.25 +"[M-H-C4H10O]-",1,-1,-75.08044098,77,0,0.25 +"[M-H-C6H6]-",1,-1,-79.05422621,78,0,0.25 +"[M-H-CS2]-",1,-1,-76.9514174,79,0,0.25 +"[M-H-C5H5N]-",1,-1,-80.049475177,80,0,0.25 +"[M-H-HBr]-",1,-1,-80.933437135,81,0,0.25 +"[M-H-C2F4]-",1,-1,-101.00088888,82,0,0.25 +"[M-H-C2F6]-",1,-1,-138.99769532,83,0,0.25 +"[M-H-C7H6O2]-",1,-1,-123.04405547,84,0,0.25 +"[M-H-HI]-",1,-1,-128.919574035,85,0,0.25 +"[M-H-H6O3]-",1,-1,-55.0389701,87,0,0.25 +"[M-H-H8O4]-",1,-1,-73.0495348,88,0,0.25 +"[M-H-H10O5]-",1,-1,-91.0600995,89,0,0.25 +"[M-H-H12O6]-",1,-1,-109.0706642,90,0,0.25 +"[M-H-H14O7]-",1,-1,-127.0812289,91,0,0.25 +"[M-H-CH6O3]-",1,-1,-67.0389701,93,0,0.25 +"[M-H-CH4O2]-",1,-1,-49.0284054,94,0,0.25 +"[M-H-NaOH]-",1,-1,-40.999783365,95,0,0.25 +"[M-H-KOH]-",1,-1,-56.973723065,96,0,0.25 |
| b |
| diff -r 9c037181588e -r 1c30ff90f3ae test-data/CASMI_extended_POS_rules.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/CASMI_extended_POS_rules.csv Fri Apr 07 07:42:18 2017 -0400 |
| [ |
| b'@@ -0,0 +1,312 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,201,0,0.25\r\n+"[M+3H-C2H5Cl]3+",1,3,-60.986149895,202,0,0.25\r\n+"[M+H-C5H4]+",1,1,-63.02402414,203,0,0.25\r\n+"[M+2H-C5H4]2+",1,2,-62.01674814,204,0,0.25\r\n+"[M+3H-C5H4]3+",1,3,-61.00947214,205,0,0.25\r\n+"[M+H-SO2]+",1,1,-62.95462396,206,0,0.25\r\n+"[M+2H-SO2]2+",1,2,-61.94734796,207,0,0.25\r\n+"[M+3H-SO2]3+",1,3,-60.94007196,208,0,0.25\r\n+"[M+H-C5H8]+",1,1,-67.05532428,209,0,0.25\r\n+"[M+2H-C5H8]2+",1,2,-66.04804828,210,0,0.25\r\n+"[M+3H-C5H8]3+",1,3,-65.04077228,211,0,0.25\r\n+"[M+H-C5H12]+",1,1,-71.08662442,212,0,0.25\r\n+"[M+2H-C5H12]2+",1,2,-70.07934842,213,0,0.25\r\n+"[M+3H-C5H12]3+",1,3,-69.07207242,214,0,0.25\r\n+"[M+H-C3H6O2]+",1,1,-73.02950347,215,0,0.25\r\n+"[M+2H-C3H6O2]2+",1,2,-72.02222747,216,0,0.25\r\n+"[M+3H-C3H6O2]3+",1,3,-71.01495147,217,0,0.25\r\n+"[M+H-C4H10O]+",1,1,-73.06588898,218,0,0.25\r\n+"[M+2H-C4H10O]2+",1,2,-72.05861298,219,0,0.25\r\n+"[M+3H-C4H10O]3+",1,3,-71.05133698,220,0,0.25\r\n+"[M+H-C6H6]+",1,1,-77.03967421,221,0,0.25\r\n+"[M+2H-C6H6]2+",1,2,-76.03239821,222,0,0.25\r\n+"[M+3H-C6H6]3+",1,3,-75.02512221,223,0,0.25\r\n+"[M+H-CS2]+",1,1,-74.9368654,224,0,0.25\r\n+"[M+2H-CS2]2+",1,2,-73.9295894,225,0,0.25\r\n+"[M+3H-CS2]3+",1,3,-72.9223134,226,0,0.25\r\n+"[M+H-C5H5N]+",1,1,-78.034923177,227,0,0.25\r\n+"[M+2H-C5H5N]2+",1,2,-77.027647177,228,0,0.25\r\n+"[M+3H-C5H5N]3+",1,3,-76.020371177,229,0,0.25\r\n+"[M+H-HBr]+",1,1,-78.918885135,230,0,0.25\r\n+"[M+2H-HBr]2+",1,2,-77.911609135,231,0,0.25\r\n+"[M+3H-HBr]3+",1,3,-76.904333135,232,0,0.25\r\n+"[M+H-C2F4]+",1,1,-98.98633688,233,0,0.25\r\n+"[M+2H-C2F4]2+",1,2,-97.97906088,234,0,0.25\r\n+"[M+3H-C2F4]3+",1,3,-96.97178488,235,0,0.25\r\n+"[M+H-C2F6]+",1,1,-136.98314332,236,0,0.25\r\n+"[M+2H-C2F6]2+",1,2,-135.97586732,237,0,0.25\r\n+"[M+3H-C2F6]3+",1,3,-134.96859132,238,0,0.25\r\n+"[M+H-C7H6O2]+",1,1,-121.02950347,239,0,0.25\r\n+"[M+2H-C7H6O2]2+",1,2,-120.02222747,240,0,0.25\r\n+"[M+3H-C7H6O2]3+",1,3,-119.01495147,241,0,0.25\r\n+"[M+H-HI]+",1,1,-126.905022035,242,0,0.25\r\n+"[M+2H-HI]2+",1,2,-125.897746035,243,0,0.25\r\n+"[M+3H-HI]3+",1,3,-124.890470035,244,0,0.25\r\n+"[M+H-H6O3]+",1,1,-53.0244181,248,0,0.25\r\n+"[M+2H-H6O3]2+",1,2,-52.0171421,249,0,0.25\r\n+"[M+3H-H6O3]3+",1,3,-51.0098661,250,0,0.25\r\n+"[M+H-H8O4]+",1,1,-71.0349828,251,0,0.25\r\n+"[M+2H-H8O4]2+",1,2,-70.0277068,252,0,0.25\r\n+"[M+3H-H8O4]3+",1,3,-69.0204308,253,0,0.25\r\n+"[M+H-H10O5]+",1,1,-89.0455475,254,0,0.25\r\n+"[M+2H-H10O5]2+",1,2,-88.0382715,255,0,0.25\r\n+"[M+3H-H10O5]3+",1,3,-87.0309955,256,0,0.25\r\n+"[M+H-H12O6]+",1,1,-107.0561122,257,0,0.25\r\n+"[M+2H-H12O6]2+",1,2,-106.0488362,258,0,0.25\r\n+"[M+3H-H12O6]3+",1,3,-105.0415602,259,0,0.25\r\n+"[M+H-H14O7]+",1,1,-125.0666769,260,0,0.25\r\n+"[M+2H-H14O7]2+",1,2,-124.0594009,261,0,0.25\r\n+"[M+3H-H14O7]3+",1,3,-123.0521249,262,0,0.25\r\n+"[M+H-CH6O3]+",1,1,-65.0244181,266,0,0.25\r\n+"[M+2H-CH6O3]2+",1,2,-64.0171421,267,0,0.25\r\n+"[M+3H-CH6O3]3+",1,3,-63.0098661,268,0,0.25\r\n+"[M+H-CH4O2]+",1,1,-47.0138534,269,0,0.25\r\n+"[M+2H-CH4O2]2+",1,2,-46.0065774,270,0,0.25\r\n+"[M+3H-CH4O2]3+",1,3,-44.9993014,271,0,0.25\r\n+"[M+H-NaOH]+",1,1,-38.985231365,272,0,0.25\r\n+"[M+2H-NaOH]2+",1,2,-37.977955365,273,0,0.25\r\n+"[M+3H-NaOH]3+",1,3,-36.970679365,274,0,0.25\r\n+"[M+H-KOH]+",1,1,-54.959171065,275,0,0.25\r\n+"[M+2H-KOH]2+",1,2,-53.951895065,276,0,0.25\r\n+"[M+3H-KOH]3+",1,3,-52.944619065,277,0,0.25\r\n' |
| b |
| diff -r 9c037181588e -r 1c30ff90f3ae test-data/faahKO-single.xset.merged.group.retcor.group.fillpeaks.RData |
| b |
| Binary file test-data/faahKO-single.xset.merged.group.retcor.group.fillpeaks.RData has changed |
| b |
| diff -r 9c037181588e -r 1c30ff90f3ae test-data/faahKO.xset.group.retcor.group.fillPeaks.annotate.dataMatrix.tsv --- a/test-data/faahKO.xset.group.retcor.group.fillPeaks.annotate.dataMatrix.tsv Wed Feb 01 12:24:04 2017 -0500 +++ b/test-data/faahKO.xset.group.retcor.group.fillPeaks.annotate.dataMatrix.tsv Fri Apr 07 07:42:18 2017 -0400 |
| b |
| b'@@ -182,7 +182,7 @@\n M212T3941\t0\t0\t1197.22500000004\t0\n M212T3970\t155.689673877202\t0\t838.732800000007\t0\n M212T3804\t0\t0\t1062.49919999995\t0\n-M213T3904\t0\t1230.08999999997\t0\t0\n+M213T3904_1\t0\t1230.08999999997\t0\t0\n M213T4087\t0\t0\t0\t1056.24000000001\n M213T3699\t0\t0\t0\t2142.48500000007\n M213T3793\t0\t3184.77499999996\t0\t0\n@@ -190,7 +190,7 @@\n M213T2688\t0\t5023.65000000018\t0\t0\n M213T3487\t8261.63499999989\t0\t0\t0\n M213T4135\t1010.12467927487\t172.279374858226\t0\t1228.52499999999\n-M213T3904\t1081.29983333335\t0\t700.103750256462\t1711.00602968181\n+M213T3904_2\t1081.29983333335\t0\t700.103750256462\t1711.00602968181\n M213T2866\t0\t9848.54499999999\t0\t0\n M213T3283\t0\t5371.08000000019\t1374.37696617401\t1789.50584149986\n M213T3836\t536.790799509607\t0\t419.296573102181\t5720.0750000002\n@@ -335,13 +335,13 @@\n M223T3313\t0\t3240.70080000003\t0\t0\n M224T4048\t0\t779.370000000007\t0\t118.093822218595\n M224T4012\t0\t0\t1216.00499999997\t0\n-M224T3097\t0\t4964.18000000017\t0\t0\n+M224T3097_1\t0\t4964.18000000017\t0\t0\n M224T3165\t0\t2834.21499999993\t0\t1599.39813285254\n M224T3761\t784.00195025327\t2252.86262342991\t2904.40800000005\t0\n M224T2739\t7904.81499999989\t0\t0\t0\n M224T2979\t16924.983409091\t0\t6208.83004073805\t1743.57335870174\n M224T2954\t4743.51500000016\t0\t0\t1737.19023073431\n-M224T3097\t0\t0\t0\t6100.36999999992\n+M224T3097_2\t0\t0\t0\t6100.36999999992\n M224T2909\t1439.22939638862\t0\t5973.60500000021\t0\n M224T3052\t0\t0\t4151.94500000015\t1483.25818381136\n M224T3074\t0\t3954.75500000014\t0\t0\n@@ -796,7 +796,7 @@\n M254T3082\t10735.4354696213\t10226.6214999999\t5000.92016733439\t1456.89586045183\n M254T3528\t0\t2067.36499999997\t0\t0\n M254T3960\t587.860834853306\t196.225263914304\t0\t1854.52499999999\n-M254T3902\t323.145865665311\t0\t0\t1369.37500000005\n+M254T3902_1\t323.145865665311\t0\t0\t1369.37500000005\n M254T2927\t0\t6479.09999999985\t0\t0\n M254T3379\t0\t4134.39975000008\t962.466461446885\t0\n M254T3261\t10767.7820000002\t0\t0\t0\n@@ -813,7 +813,7 @@\n M254T2804\t0\t5123.80999999995\t1490.36357498886\t2132.64652048757\n M254T3277\t12377.5850000004\t18560.9823750003\t9588.74205405444\t0\n M254T4105\t0\t959.345000000033\t0\t243.426297233091\n-M254T3902\t524.652370000034\t1727.2058439476\t312.233942059826\t1846.60923076924\n+M254T3902_2\t524.652370000034\t1727.2058439476\t312.233942059826\t1846.60923076924\n M255T3929\t2021.97999999995\t0\t0\t0\n M255T4074\t294.557048935163\t0\t2408.27849999992\t0\n M255T4111\t1197.45059631817\t0\t0\t2250.2645714287\n@@ -1150,9 +1150,9 @@\n M276T3077\t0\t6451.9060000001\t0\t0\n M276T3716\t0\t3369.20577777774\t0\t0\n M276T3765\t0\t1311.46999999997\t234.428194546826\t1833.9984450473\n-M276T3867\t113.552433065314\t2896.81499999999\t0\t341.188481234697\n+M276T3867_1\t113.552433065314\t2896.81499999999\t0\t341.188481234697\n M276T3496\t4892.33507471811\t2874.90499999993\t1606.89745276928\t1797.86632777711\n-M276T3867\t1347.32150000002\t0\t0\t732.510425074664\n+M276T3867_2\t1347.32150000002\t0\t0\t732.510425074664\n M276T3778\t4684.04500000006\t2919.65750737896\t2967.27412953143\t442.895784592734\n M276T4109\t2001.54364285715\t112.874592384196\t1030.71045061812\t108.538311136801\n M276T4005\t777.722166666639\t0\t0\t0\n@@ -1735,10 +1735,10 @@\n M309T4180\t414.632134822523\t1144.01499999997\t0\t0\n M309T3985\t3163.99186583752\t2281.47059809708\t28385.9576956521\t3273.90087643464\n M309T4149\t0\t0\t0\t1256.59462499993\n-M310T3461\t36258.0630753291\t534331.077923075\t63364.2486390118\t21058.5811919054\n+M310T3461_1\t36258.0630753291\t534331.077923075\t63364.2486390118\t21058.5811919054\n M310T4201\t270.096443583602\t1540.0349421739\t0\t904.533874999991\n M310T2926\t135328.05026087\t82033.1251526926\t107511.434843213\t95307.4161584627\n-M310T3461\t72928.5388695646\t9060.4834167398\t43575.164528626\t89770.4875909093\n+M310T3461_2\t72928.5388695646\t9060.4834167398\t43575.164528626\t89770.4875909093\n M310T3484\t9991.07390724506\t43590.0440000006\t8651.98130329359\t21231.974486064\n M310T2522\t0\t0\t0\t5998.64499999992\n M310T2584\t0\t2560.33999999994\t4509.75360000004\t6593.34499999991\n@@ -1977,7 +1977,7 @@\n M323T3910\t1294.54365263385\t3196.68264006145\t3444.34490000008\t0\n M323T3351\t790.706305477901\t893.615000000031\t0\t0\n M323T4059\t0\t1408.5\t0\t138.14096421908\n-M324T2708\t886.898519467729\t7570.'..b'.6847900913\t27771.4461176469\t0\n+M578T3296_1\t271.769310365731\t1612.6847900913\t27771.4461176469\t0\n M578T4169\t0\t0\t0\t10191.2799999998\n M578T4183\t6566.73999999985\t0\t1509.30034256449\t0\n M578T3335\t0\t0\t0\t1730.88999999996\n@@ -7474,8 +7474,8 @@\n M578T2627\t5897.73120000005\t0\t1703.4085001727\t0\n M578T2823\t0\t625.429689257525\t1158.75224564973\t5087.5827857142\n M578T3397\t0\t4460.2499999999\t10944.7357499998\t0\n-M578T3296\t0\t0\t15139.7624999995\t0\n-M578T3525\t0\t1725.52526263461\t0\t1151.83999999997\n+M578T3296_2\t0\t0\t15139.7624999995\t0\n+M578T3525_1\t0\t1725.52526263461\t0\t1151.83999999997\n M578T2863\t0\t1137.88610086279\t0\t6125.10892307694\n M578T3664\t7866.61966260738\t21057.6567387522\t6694.21440000006\t0\n M578T3753\t0\t0\t3444.56499999992\t2161.58040689481\n@@ -7498,7 +7498,7 @@\n M578T3711\t1207.73596507746\t9443.91285714301\t2726.85964479057\t0\n M578T3834\t1797006.00545455\t68270.738466602\t1461649.20674704\t0\n M578T3122\t4278.01062753194\t0\t5516.62499999987\t0\n-M578T3525\t0\t0\t0\t1544.65499999996\n+M578T3525_2\t0\t0\t0\t1544.65499999996\n M578T2710\t0\t395.07572393755\t0\t1910.62079999991\n M579T2700\t0\t0\t3680.87999999991\t0\n M579T2614\t3906.23999999991\t657.299999999975\t0\t0\n@@ -7609,7 +7609,7 @@\n M582T3926\t4325.65999999994\t0\t463.655372755083\t5775.09398174128\n M582T4177\t3740.13272727271\t0\t3500.99507055468\t0\n M582T3473\t34318.7630769232\t21818.0567062937\t36387.3919458424\t846.135486558828\n-M582T3848\t3706.26414215403\t2375.73727172652\t21326.255\t2184.38504961376\n+M582T3848_1\t3706.26414215403\t2375.73727172652\t21326.255\t2184.38504961376\n M582T3351\t7252.23586542253\t1818.08994825976\t11770.3650000004\t0\n M582T3377\t3313.49155065192\t5288.55970033321\t15756.42\t14687.8036690723\n M582T3987\t0\t0\t3724.57552935945\t13385.4449999997\n@@ -7624,7 +7624,7 @@\n M582T3970\t9966.41430434512\t59220.4082294011\t4932.63698859328\t160504.868090909\n M582T3725\t3174.45340524226\t6887.56500000009\t0\t0\n M582T2894\t3208.38147928956\t0\t18092.0015833333\t0\n-M582T3848\t0\t4178.55000000015\t0\t1785.97268831806\n+M582T3848_2\t0\t4178.55000000015\t0\t1785.97268831806\n M582T4185\t4236.45500000015\t0\t5535.18404372073\t2135.5308045648\n M583T3933\t0\t0\t3458.3342857142\t0\n M583T2617\t514.305183361411\t0\t2012.55274236495\t2694.92999999996\n@@ -7816,7 +7816,7 @@\n M588T2863\t1455.41158765376\t1793.53455598184\t3201.0517261516\t10308.1060833333\n M588T3201\t6222.43999999992\t0\t0\t0\n M589T2744\t1867.14191786999\t6209.25866666675\t2045.34607773754\t0\n-M589T3027\t0\t4485.2899999999\t0\t1036.25051933095\n+M589T3027_1\t0\t4485.2899999999\t0\t1036.25051933095\n M589T2708\t3250.50500000011\t0\t0\t0\n M589T2669\t0\t3514.98999999995\t0\t2274.88465862483\n M589T3041\t0\t0\t3453.95499999992\t1584.46338550673\n@@ -7828,7 +7828,7 @@\n M589T3399\t0\t0\t1752.61333333336\t0\n M589T4171\t924.796799999954\t0\t0\t142.379847026552\n M589T4211\t141.349674086105\t0\t971.776285714342\t0\n-M589T3027\t2604.25713408938\t0\t1469.671409555\t5762.33000000006\n+M589T3027_2\t2604.25713408938\t0\t1469.671409555\t5762.33000000006\n M589T4078\t2508.69499999994\t0\t0\t1585.0993232845\n M589T3066\t5769.66878713768\t8291.36999999989\t0\t0\n M589T3098\t2178.48371465977\t0\t10767.6181666668\t1971.07232973347\n@@ -7998,7 +7998,7 @@\n M595T2655\t0\t765.239870733435\t1233.21808896358\t4982.95999999993\n M595T2603\t60509.4258518521\t6683.93068686915\t19792.9643102431\t3440.16429307587\n M595T3000\t82683.667879537\t316155.893850002\t1007151.89818182\t60036.1307137129\n-M595T2650\t832.837290081034\t0\t6429.01999999985\t844.334372955168\n+M595T2650_1\t832.837290081034\t0\t6429.01999999985\t844.334372955168\n M595T3780\t127545.669125001\t4735.55583624839\t149919.4475625\t4845.0498192778\n M595T4205\t6956.14718749993\t4852.197541911\t3880.19666617499\t3978.9811068691\n M595T2543\t0\t600.864000000001\t4907.84000000017\t0\n@@ -8009,7 +8009,7 @@\n M595T2520\t907.635555555574\t5554.18500000003\t583.703555555567\t0\n M595T2753\t0\t1373.37213215749\t0\t1687.07000000006\n M595T4209\t1174.82660389549\t2642.1377457943\t8118.931777778\t3677.34004605241\n-M595T2650\t0\t2237.94999999995\t0\t0\n+M595T2650_2\t0\t2237.94999999995\t0\t0\n M595T2818\t0\t0\t3530.63999999992\t0\n M595T3782\t17889.5149999996\t0\t31617.7414604441\t424.113789166877\n M595T3326\t508.758898013783\t1840.43999999996\t0\t0\n' |
| b |
| diff -r 9c037181588e -r 1c30ff90f3ae test-data/faahKO.xset.group.retcor.group.fillPeaks.annotate.rules.dataMatrix.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/faahKO.xset.group.retcor.group.fillPeaks.annotate.rules.dataMatrix.tsv Fri Apr 07 07:42:18 2017 -0400 |
| b |
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|
| b |
| diff -r 9c037181588e -r 1c30ff90f3ae test-data/faahKO.xset.group.retcor.group.fillPeaks.annotate.rules.variableMetadata.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/faahKO.xset.group.retcor.group.fillPeaks.annotate.rules.variableMetadata.tsv Fri Apr 07 07:42:18 2017 -0400 |
| [ |
| b'@@ -0,0 +1,8158 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|
| b |
| diff -r 9c037181588e -r 1c30ff90f3ae test-data/faahKO.xset.group.retcor.group.fillPeaks.annotate.variableMetadata.tsv --- a/test-data/faahKO.xset.group.retcor.group.fillPeaks.annotate.variableMetadata.tsv Wed Feb 01 12:24:04 2017 -0500 +++ b/test-data/faahKO.xset.group.retcor.group.fillPeaks.annotate.variableMetadata.tsv Fri Apr 07 07:42:18 2017 -0400 |
| b |
| b'@@ -1,8158 +1,8158 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| diff -r 9c037181588e -r 1c30ff90f3ae tool_dependencies.xml --- a/tool_dependencies.xml Wed Feb 01 12:24:04 2017 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,12 +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-camera" version="1.26.0"> - <repository changeset_revision="fd308c76626b" name="package_bioconductor_camera_1_26_0" owner="lecorguille" toolshed="https://toolshed.g2.bx.psu.edu" /> - </package> - <package name="graphicsmagick" version="1.3.20"> - <repository changeset_revision="f2855f4cbc8f" name="package_graphicsmagick_1_3_20" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> - </package> -</tool_dependency> |
