# HG changeset patch
# User lecorguille
# Date 1556533384 14400
# Node ID f1a287a8509be34b2189901697ea6e8f609199df
# Parent  7c4e3703b45a94ebbc63216a43356535a4ed9ce9
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a5136bfc124956893f4f0c91808d1c0d78c4ea01

diff -r 7c4e3703b45a -r f1a287a8509b lib.r
--- a/lib.r	Tue Mar 12 11:00:37 2019 -0400
+++ b/lib.r	Mon Apr 29 06:23:04 2019 -0400
@@ -333,7 +333,7 @@
     files[exists] <- sub("//","/",files[exists])
 
     # WHAT IS ON THE FILESYSTEM
-    filesystem_filepaths <- system(paste0("find \"$PWD/",directory,"\" -not -name '\\.*' -not -path '*conda-env*' -type f -name \"*\""), intern=T)
+    filesystem_filepaths <- system(paste0("find \"",getwd(),"/",directory,"\" -not -name '\\.*' -not -path '*conda-env*' -type f -name \"*\""), intern=T)
     filesystem_filepaths <- filesystem_filepaths[grep(filepattern, filesystem_filepaths, perl=T)]
 
     # COMPARISON