Mercurial > repos > lecorguille > xcms_plot_chromatogram
comparison lib.r @ 12:10315a095169 draft
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a5136bfc124956893f4f0c91808d1c0d78c4ea01
| author | lecorguille |
|---|---|
| date | Mon, 29 Apr 2019 06:09:00 -0400 |
| parents | 5f0327d6f474 |
| children | 9a5b4a1b9880 |
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| 11:5f0327d6f474 | 12:10315a095169 |
|---|---|
| 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()) |