Mercurial > repos > lecorguille > xcms_retcor

comparison lib.r @ 43:221a8c6de94a draft

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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a5136bfc124956893f4f0c91808d1c0d78c4ea01
author lecorguille
date Mon, 29 Apr 2019 06:12:54 -0400
parents feb216e6aef7
children 1986c48d86ce
comparison
equal deleted inserted replaced
42:feb216e6aef7 43:221a8c6de94a
67 chromBPI_merged <- chromBPI 67 chromBPI_merged <- chromBPI
68 chromTIC_adjusted_merged <- chromTIC_adjusted 68 chromTIC_adjusted_merged <- chromTIC_adjusted
69 chromBPI_adjusted_merged <- chromBPI_adjusted 69 chromBPI_adjusted_merged <- chromBPI_adjusted
70 } else { 70 } else {
71 if (is(xdata, "XCMSnExp")) xdata_merged <- c(xdata_merged,xdata) 71 if (is(xdata, "XCMSnExp")) xdata_merged <- c(xdata_merged,xdata)
72 else if (is(xdata, "OnDiskMSnExp")) xdata_merged <- .concatenate_OnDiskMSnExp(xdata_merged,xdata) 72 else if (is(xdata, "OnDiskMSnExp")) xdata_merged <- xcms:::.concatenate_OnDiskMSnExp(xdata_merged,xdata)
73 else stop("\n\nERROR: The RData either a OnDiskMSnExp object called raw_data or a XCMSnExp object called xdata") 73 else stop("\n\nERROR: The RData either a OnDiskMSnExp object called raw_data or a XCMSnExp object called xdata")
74 74
75 singlefile_merged <- c(singlefile_merged,singlefile) 75 singlefile_merged <- c(singlefile_merged,singlefile)
76 md5sumList_merged$origin <- rbind(md5sumList_merged$origin,md5sumList$origin) 76 md5sumList_merged$origin <- rbind(md5sumList_merged$origin,md5sumList$origin)
77 sampleNamesList_merged$sampleNamesOrigin <- c(sampleNamesList_merged$sampleNamesOrigin,sampleNamesList$sampleNamesOrigin) 77 sampleNamesList_merged$sampleNamesOrigin <- c(sampleNamesList_merged$sampleNamesOrigin,sampleNamesList$sampleNamesOrigin)
331 exists <- file.exists(files_abs) 331 exists <- file.exists(files_abs)
332 files[exists] <- files_abs[exists] 332 files[exists] <- files_abs[exists]
333 files[exists] <- sub("//","/",files[exists]) 333 files[exists] <- sub("//","/",files[exists])
334 334
335 # WHAT IS ON THE FILESYSTEM 335 # WHAT IS ON THE FILESYSTEM
336 filesystem_filepaths <- system(paste0("find \"$PWD/",directory,"\" -not -name '\\.*' -not -path '*conda-env*' -type f -name \"*\""), intern=T) 336 filesystem_filepaths <- system(paste0("find \"",getwd(),"/",directory,"\" -not -name '\\.*' -not -path '*conda-env*' -type f -name \"*\""), intern=T)
337 filesystem_filepaths <- filesystem_filepaths[grep(filepattern, filesystem_filepaths, perl=T)] 337 filesystem_filepaths <- filesystem_filepaths[grep(filepattern, filesystem_filepaths, perl=T)]
338 338
339 # COMPARISON 339 # COMPARISON
340 if (!is.na(table(filesystem_filepaths %in% files)["FALSE"])) { 340 if (!is.na(table(filesystem_filepaths %in% files)["FALSE"])) {
341 write("\n\nERROR: List of the files which will not be imported by xcmsSet",stderr()) 341 write("\n\nERROR: List of the files which will not be imported by xcmsSet",stderr())