Mercurial > repos > lecorguille > xcms_export_samplemetadata
comparison lib.r @ 7:f39cd33a73a6 draft
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a5136bfc124956893f4f0c91808d1c0d78c4ea01
| author | lecorguille |
|---|---|
| date | Mon, 29 Apr 2019 06:32:48 -0400 |
| parents | 14316f8f67a2 |
| children | c684ccd89267 |
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| 6:14316f8f67a2 | 7:f39cd33a73a6 |
|---|---|
| 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()) |