Mercurial > repos > lecorguille > xcms_summary

comparison lib.r @ 24:acc0a4a366c1 draft

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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a5136bfc124956893f4f0c91808d1c0d78c4ea01
author lecorguille
date Mon, 29 Apr 2019 06:31:35 -0400
parents 7941015d6fc0
children acc66e5c23d7
comparison
equal deleted inserted replaced
23:08f5203ef8c1 24:acc0a4a366c1
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())