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planemo upload commit 98cb24e57c0ce8ac3294e8c7e87aee337ac29f62
author lecorguille
date Thu, 28 Jul 2016 11:11:38 -0400
parents 9f1e18bc8ce3
children 03fdfbd914ab
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1 ##
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2 ## This function launch IPO functions to get the best parameters for xcmsSet
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3 ## A sample among the whole dataset is used to save time
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4 ##
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5 ipo4xcmsSet = function(directory, parametersOutput, listArguments, samplebyclass=4) {
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6 setwd(directory)
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8 files = list.files(".", recursive=T) # "KO/ko15.CDF" "KO/ko16.CDF" "WT/wt15.CDF" "WT/wt16.CDF"
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9 files_classes = basename(dirname(files)) # "KO", "KO", "WT", "WT"
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11 mzmlfile = files
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12 if (samplebyclass > 0) {
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13 #random selection of N files for IPO in each class
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14 classes<-unique(basename(dirname(files)))
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15 mzmlfile = NULL
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16 for (class_i in classes){
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17 files_class_i = files[files_classes==class_i]
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18 if (samplebyclass > length(files_class_i)) {
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19 mzmlfile = c(mzmlfile, files_class_i)
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20 } else {
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21 mzmlfile = c(mzmlfile,sample(files_class_i,samplebyclass))
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22 }
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23 }
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24 }
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25 #@TODO: else, must we keep the RData to been use directly by group?
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27 cat("\t\tSamples used:\n")
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28 print(mzmlfile)
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30 peakpickingParameters = getDefaultXcmsSetStartingParams(listArguments[["method"]]) #get default parameters of IPO
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32 # filter listArguments to only get releavant parameters and complete with those that are not declared
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33 peakpickingParametersUser = c(listArguments[names(listArguments) %in% names(peakpickingParameters)], peakpickingParameters[!(names(peakpickingParameters) %in% names(listArguments))])
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34 peakpickingParametersUser$verbose.columns = TRUE
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36 #peakpickingParametersUser$profparam <- list(step=0.005) #not yet used by IPO have to think of it for futur improvement
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37 resultPeakpicking = optimizeXcmsSet(mzmlfile, peakpickingParametersUser, subdir="IPO_results") #some images generated by IPO
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39 # export
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40 resultPeakpicking_best_settings_parameters = resultPeakpicking$best_settings$parameters[!(names(resultPeakpicking$best_settings$parameters) %in% c("nSlaves","verbose.columns"))]
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41 write.table(resultPeakpicking_best_settings_parameters, file=parametersOutput, sep="\t",row.names=FALSE) #can be read by user
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43 }
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48 ##
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49 ## This function check if xcms will found all the files
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50 ##
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51 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr ABiMS TEAM
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52 checkFilesCompatibilityWithXcms <- function(directory) {
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53 cat("Checking files filenames compatibilities with xmcs...\n")
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54 # WHAT XCMS WILL FIND
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55 filepattern <- c("[Cc][Dd][Ff]", "[Nn][Cc]", "([Mm][Zz])?[Xx][Mm][Ll]","[Mm][Zz][Dd][Aa][Tt][Aa]", "[Mm][Zz][Mm][Ll]")
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56 filepattern <- paste(paste("\\.", filepattern, "$", sep = ""),collapse = "|")
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57 info <- file.info(directory)
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58 listed <- list.files(directory[info$isdir], pattern = filepattern,recursive = TRUE, full.names = TRUE)
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59 files <- c(directory[!info$isdir], listed)
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60 files_abs <- file.path(getwd(), files)
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61 exists <- file.exists(files_abs)
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62 files[exists] <- files_abs[exists]
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63 files[exists] <- sub("//","/",files[exists])
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64
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65 # WHAT IS ON THE FILESYSTEM
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66 filesystem_filepaths=system(paste("find $PWD/",directory," -not -name '\\.*' -not -path '*conda-env*' -type f -name \"*\"", sep=""), intern=T)
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67 filesystem_filepaths=filesystem_filepaths[grep(filepattern, filesystem_filepaths, perl=T)]
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68
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69 # COMPARISON
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70 if (!is.na(table(filesystem_filepaths %in% files)["FALSE"])) {
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71 write("\n\nERROR: List of the files which will not be imported by xcmsSet",stderr())
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72 write(filesystem_filepaths[!(filesystem_filepaths %in% files)],stderr())
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73 stop("\n\nERROR: One or more of your files will not be import by xcmsSet. It may due to bad characters in their filenames.")
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74
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75 }
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76 }
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80 ##
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81 ## This function check if XML contains special caracters. It also checks integrity and completness.
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82 ##
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83 #@author Misharl Monsoor misharl.monsoor@sb-roscoff.fr ABiMS TEAM
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84 checkXmlStructure <- function (directory) {
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85 cat("Checking XML structure...\n")
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86
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87 cmd=paste("IFS=$'\n'; for xml in $(find",directory,"-not -name '\\.*' -not -path '*conda-env*' -type f -iname '*.*ml*'); do if [ $(xmllint --nonet --noout \"$xml\" 2> /dev/null; echo $?) -gt 0 ]; then echo $xml;fi; done;")
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88 capture=system(cmd,intern=TRUE)
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89
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90 if (length(capture)>0){
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91 #message=paste("The following mzXML or mzML file is incorrect, please check these files first:",capture)
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92 write("\n\nERROR: The following mzXML or mzML file(s) are incorrect, please check these files first:", stderr())
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93 write(capture, stderr())
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94 stop("ERROR: xcmsSet cannot continue with incorrect mzXML or mzML files")
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95 }
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96
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97 }