v1.12.0+galaxy1 (#33)

* Default offsets values able mzXML files We can run mzXML files with default values here for offsets... Can be good to remove them, but it may be produce an error after that should be managed ! * Bug fix for purityA offsets * Add missing bracket * Close bracket * flagRemove exit updated, update shed yml, update readme * Make flagRemove.R rdata object backward compatible
computational-metabolomics · Dec 5, 2019 · 20d432c · 20d432c
1 parent cb903cd
commit 20d432c
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diff --git a/README.rst b/README.rst
@@ -3,13 +3,13 @@ msPurity for Galaxy
 |Build Status (Travis)| |Git| |Bioconda| |License|
 
 
-Version v1.12.0+galaxy0
+Version v1.12.0+galaxy1
 ------
 
   - msPurity
      - bioconductor-mspurity v1.12.0
   - Galaxy tools
-     - v0
+     - v1
 
 About
 ------
@@ -55,6 +55,12 @@ Authors, contributors & contacts
 
 Changes
 -------------------------
+v1.12.0-galaxy1
+  - Bug fix (offsets were not being automatically selected for purityA) thanks jsaintvanne
+  - Exit script without error for flagRemove
+  - Username updated in Toolshed yaml
+
+
 v1.12.0-galaxy0
   - Updates for Bioconductor stable msPurity v1.12.0 release 
   - Additional columns added for spectral matching (for msnpy use case)

diff --git a/tools/msPurity/.shed.yml b/tools/msPurity/.shed.yml
@@ -1,4 +1,4 @@
-owner: tomnl
+owner: computational-metabolomics
 remote_repository_url: https://github.com/computational-metabolomics/mspurity-galaxy
 homepage_url:  https://github.com/computational-metabolomics/mspurity-galaxy
 categories: ["Metabolomics"]

diff --git a/tools/msPurity/flagRemove.R b/tools/msPurity/flagRemove.R
@@ -138,7 +138,7 @@ if (is.null(opt$samplelist)){
     chosen_blank <- samplelist_blank[samplelist_blank %in% xset@phenoData$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 @@ if (is.null(opt$multilist)){
     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 --git a/tools/msPurity/macros.xml b/tools/msPurity/macros.xml
@@ -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 --git a/tools/msPurity/purityA.R b/tools/msPurity/purityA.R
@@ -6,9 +6,9 @@ option_list <- list(
   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 @@ option_list <- list(
 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()