Mercurial > repos > computational-metabolomics > mspurity_createdatabase

diff flagRemove.R @ 1:600a866a510c draft

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"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 20d432cdc6326114d05c26fd51889b872513b57d"
author computational-metabolomics
date Thu, 05 Dec 2019 07:45:02 -0500
parents f52287a06c02
children 2f71b3495221
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line diff
--- a/flagRemove.R	Wed Nov 27 13:44:58 2019 -0500
+++ b/flagRemove.R	Thu Dec 05 07:45:02 2019 -0500
@@ -138,7 +138,7 @@
     chosen_blank <- samplelist_blank[samplelist_blank %in% xset@phenoData$class]
     if (length(chosen_blank)>1){
         print('ERROR: only 1 blank is currently allowed to be used with this tool')
-        exit()
+        quit()
     }
     blank_class <- as.character(chosen_blank)
     print(blank_class)
@@ -171,7 +171,7 @@
     grp_peaklist <- ffrm_out[[2]]
     removed_peaks <- ffrm_out[[3]]
 
-    save.image(file=file.path(opt$out_dir, 'xset_filtered.RData'))
+    save.image(file=file.path(opt$out_dir, 'xset_filtered.RData'), version=2)
 
     # grpid needed for mspurity ID needed for deconrank... (will clean up at some up)
     peak_pth <- file.path(opt$out_dir, 'peaklist_filtered.tsv')