# HG changeset patch
# User computational-metabolomics
# Date 1575549902 18000
# Node ID 600a866a510c818f4da37129b93582cc29f34639
# Parent  f52287a06c02fd8f33d08e1fdd6195e6323c034b
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 20d432cdc6326114d05c26fd51889b872513b57d"

diff -r f52287a06c02 -r 600a866a510c flagRemove.R
--- 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')
diff -r f52287a06c02 -r 600a866a510c macros.xml
--- a/macros.xml	Wed Nov 27 13:44:58 2019 -0500
+++ b/macros.xml	Thu Dec 05 07:45:02 2019 -0500
@@ -1,7 +1,7 @@
 <?xml version="1.0"?>
 <macros>
     <token name="@TOOL_VERSION@">1.12.0</token>
-    <token name="@GALAXY_TOOL_VERSION@">0</token>
+    <token name="@GALAXY_TOOL_VERSION@">1</token>
 
     <xml name="requirements">
         <requirements>
diff -r f52287a06c02 -r 600a866a510c purityA.R
--- a/purityA.R	Wed Nov 27 13:44:58 2019 -0500
+++ b/purityA.R	Thu Dec 05 07:45:02 2019 -0500
@@ -6,9 +6,9 @@
   make_option(c("-o", "--out_dir"), type="character"),
   make_option("--mzML_files", type="character"),
   make_option("--galaxy_names", type="character"),
-  make_option("--minOffset", default=0.5),
-  make_option("--maxOffset", default=0.5),
-  make_option("--ilim", default=0.05),
+  make_option("--minOffset", type="numeric"),
+  make_option("--maxOffset", type="numeric"),
+  make_option("--ilim", type="numeric"),
   make_option("--iwNorm", default="none", type="character"),
   make_option("--exclude_isotopes", action="store_true"),
   make_option("--isotope_matrix", type="character"),
@@ -22,18 +22,26 @@
 opt <- parse_args(OptionParser(option_list=option_list))
 print(opt)
 
-minOffset = as.numeric(opt$minOffset)
-maxOffset = as.numeric(opt$maxOffset)
 
 if (opt$iwNorm=='none'){
     iwNorm = FALSE
     iwNormFun = NULL
 }else if (opt$iwNorm=='gauss'){
     iwNorm = TRUE
-    iwNormFun = msPurity::iwNormGauss(minOff=-minOffset, maxOff=maxOffset)
+    if (is.null(opt$minOffset) || is.null(opt$maxOffset)){
+      print('User has to define offsets if using Gaussian normalisation')
+    }else{
+      iwNormFun = msPurity::iwNormGauss(minOff=-as.numeric(opt$minOffset), 
+                                      maxOff=as.numeric(opt$maxOffset))
+    }
 }else if (opt$iwNorm=='rcosine'){
     iwNorm = TRUE
-    iwNormFun = msPurity::iwNormRcosine(minOff=-minOffset, maxOff=maxOffset)
+    if (is.null(opt$minOffset) || is.null(opt$maxOffset)){
+      print('User has to define offsets if using R-cosine normalisation')
+    }else{
+      iwNormFun = msPurity::iwNormRcosine(minOff=-as.numeric(opt$minOffset), 
+                                          maxOff=as.numeric(opt$maxOffset))
+    }
 }else if (opt$iwNorm=='QE5'){
     iwNorm = TRUE
     iwNormFun = msPurity::iwNormQE.5()