# HG changeset patch
# User computational-metabolomics
# Date 1726230267 0
# Node ID 13034c3886f242ede18c3890be273564d09ed111
# Parent  374022b7b4692dc2b64ddc8cf161fd33fc1fa681
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f10386dee95f3b1fbc8d1eeec52d450381ba89c5

diff -r 374022b7b469 -r 13034c3886f2 README.rst
--- a/README.rst	Thu Jun 13 11:36:53 2024 +0000
+++ b/README.rst	Fri Sep 13 12:24:27 2024 +0000
@@ -3,13 +3,13 @@
 |Git| |Bioconda| |License|
 
 
-Version v1.28.0+galaxy0
+Version v1.28.0+galaxy1
 ------------------------
 
   - msPurity
      - bioconductor-mspurity v1.28.0
   - Galaxy tools
-     - v0
+     - v1
 
 About
 ------
@@ -52,6 +52,10 @@
 
 Changes
 -------------------------
+v1.28.0-galaxy1
+  - Further fix for purityX galaxy tool (https://github.com/computational-metabolomics/mspurity-galaxy/issues/53) 
+  - Fix for purityA file naming (https://github.com/computational-metabolomics/mspurity-galaxy/issues/56)
+
 v1.28.0-galaxy0
   - Version bump to v1.28.0
   - createMSP now uses the median precursor MZ and precursor RT in the MSP files
diff -r 374022b7b469 -r 13034c3886f2 purityA.R
--- a/purityA.R	Thu Jun 13 11:36:53 2024 +0000
+++ b/purityA.R	Fri Sep 13 12:24:27 2024 +0000
@@ -124,7 +124,7 @@
 print(pa)
 save(pa, file = file.path(opt$out_dir, "purityA_output.RData"))
 
-pa@puritydf$filename <- sapply(pa@puritydf$fileid, function(x) names(pa@fileList)[as.integer(x)])
+pa@puritydf$filename <- sapply(as.character(pa@puritydf$fileid), function(x) names(pa@fileList)[as.integer(x)])
 
 print(head(pa@puritydf))
 write.table(pa@puritydf, file.path(opt$out_dir, "purityA_output.tsv"), row.names = FALSE, sep = "\t")
diff -r 374022b7b469 -r 13034c3886f2 purityX.R
--- a/purityX.R	Thu Jun 13 11:36:53 2024 +0000
+++ b/purityX.R	Fri Sep 13 12:24:27 2024 +0000
@@ -16,7 +16,6 @@
   make_option("--singleFile", default = 0),
   make_option("--cores", default = 4),
   make_option("--xgroups", type = "character"),
-  make_option("--rdata_name", default = "xset"),
   make_option("--camera_xcms", default = "xset"),
   make_option("--files", type = "character"),
   make_option("--galaxy_files", type = "character"),
@@ -63,10 +62,10 @@
   rtraw_columns <- TRUE
 }
 
-loadRData <- function(rdata_path, xset_name) {
+loadRData <- function(rdata_path, xnames) {
   # loads an RData file, and returns the named xset object if it is there
   load(rdata_path)
-  return(get(ls()[ls() == xset_name]))
+  return(get(ls()[ls() %in% xnames]))
 }
 
 
@@ -90,7 +89,7 @@
   }
 }
 
-target_obj <- loadRData(opt$xset_path, opt$rdata_name)
+target_obj <- loadRData(opt$xset_path, c('xset', 'xa', 'xdata'))
 
 if (opt$camera_xcms == "camera") {
   xset <- target_obj@xcmsSet
diff -r 374022b7b469 -r 13034c3886f2 purityX.xml
--- a/purityX.xml	Thu Jun 13 11:36:53 2024 +0000
+++ b/purityX.xml	Fri Sep 13 12:24:27 2024 +0000
@@ -18,11 +18,7 @@
                 --xgroups='$xgroups.xgroups_value'
             #end if
             --camera_xcms=$camera_xcms
-            #if $camera_xcms == "camera"
-                --rdata_name=xa
-            #else
-                --rdata_name=xset
-            #end if
+
             --iwNorm=$iw_norm
             --ilim=$ilim
             #if $isotopes.isotopes == "exclude_default"