# HG changeset patch
# User lecorguille
# Date 1556533705 14400
# Node ID fe4002ac5193d28922f8bfe9922795d61acac52d
# Parent  6842c495da6d43be96d3374e02e7df752bfd323c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a5136bfc124956893f4f0c91808d1c0d78c4ea01

diff -r 6842c495da6d -r fe4002ac5193 lib.r
--- a/lib.r	Tue Apr 09 12:20:23 2019 -0400
+++ b/lib.r	Mon Apr 29 06:28:25 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