# HG changeset patch
# User lecorguille
# Date 1556532867 14400
# Node ID eeade1310758492513d897bc1ac1eb7e8b808579
# Parent  a98dbb09fed192209e7a5e8ce137163f01587451
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a5136bfc124956893f4f0c91808d1c0d78c4ea01

diff -r a98dbb09fed1 -r eeade1310758 README.rst
--- a/README.rst	Fri Feb 08 10:03:17 2019 -0500
+++ b/README.rst	Mon Apr 29 06:14:27 2019 -0400
@@ -2,9 +2,11 @@
 Changelog/News
 --------------
 
-**Version 3.4.3.0 - 08/02/2019**
+.. _News: https://bioconductor.org/packages/release/bioc/news/xcms/NEWS
 
-- UPGRADE: upgrade the xcms version from 3.0.0 to 3.4.3
+**Version 3.4.4.0 - 08/02/2019**
+
+- UPGRADE: upgrade the xcms version from 3.0.0 to 3.4.4 (see XCMS News_)
 
 - BUGFIX: issue with Inf values in the exported DataMatrix: https://github.com/sneumann/xcms/issues/323#issuecomment-433044378
 
diff -r a98dbb09fed1 -r eeade1310758 abims_xcms_fillPeaks.xml
--- a/abims_xcms_fillPeaks.xml	Fri Feb 08 10:03:17 2019 -0500
+++ b/abims_xcms_fillPeaks.xml	Mon Apr 29 06:14:27 2019 -0400
@@ -230,13 +230,14 @@
 Changelog/News
 --------------
 
-**Version 3.4.3.0 - 08/02/2019**
+.. _News: https://bioconductor.org/packages/release/bioc/news/xcms/NEWS
 
-- UPGRADE: upgrade the xcms version from 3.0.0 to 3.4.3
+**Version 3.4.4.0 - 08/02/2019**
+
+- UPGRADE: upgrade the xcms version from 3.0.0 to 3.4.4 (see XCMS News_)
 
 - BUGFIX: issue with Inf values in the exported DataMatrix: https://github.com/sneumann/xcms/issues/323#issuecomment-433044378
 
-
 **Version 3.0.0.2 - 09/11/2018**
 
 - BUGFIX: issue when the vector at peakidx is too long and is written in a new line during the export of the peaklist
diff -r a98dbb09fed1 -r eeade1310758 lib.r
--- a/lib.r	Fri Feb 08 10:03:17 2019 -0500
+++ b/lib.r	Mon Apr 29 06:14:27 2019 -0400
@@ -69,7 +69,7 @@
             chromBPI_adjusted_merged <- chromBPI_adjusted
         } else {
             if (is(xdata, "XCMSnExp")) xdata_merged <- c(xdata_merged,xdata)
-            else if (is(xdata, "OnDiskMSnExp")) xdata_merged <- .concatenate_OnDiskMSnExp(xdata_merged,xdata)
+            else if (is(xdata, "OnDiskMSnExp")) xdata_merged <- xcms:::.concatenate_OnDiskMSnExp(xdata_merged,xdata)
             else stop("\n\nERROR: The RData either a OnDiskMSnExp object called raw_data or a XCMSnExp object called xdata")
 
             singlefile_merged <- c(singlefile_merged,singlefile)
@@ -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
diff -r a98dbb09fed1 -r eeade1310758 macros_xcms.xml
--- a/macros_xcms.xml	Fri Feb 08 10:03:17 2019 -0500
+++ b/macros_xcms.xml	Mon Apr 29 06:14:27 2019 -0400
@@ -1,7 +1,7 @@
 <?xml version="1.0"?>
 <macros>
 
-    <token name="@WRAPPER_VERSION@">3.4.3</token>
+    <token name="@WRAPPER_VERSION@">3.4.4</token>
     <xml name="requirements">
         <requirements>
             <requirement type="package" version="@WRAPPER_VERSION@">bioconductor-xcms</requirement>
diff -r a98dbb09fed1 -r eeade1310758 xcms_fillpeaks.r
--- a/xcms_fillpeaks.r	Fri Feb 08 10:03:17 2019 -0500
+++ b/xcms_fillpeaks.r	Mon Apr 29 06:14:27 2019 -0400
@@ -103,7 +103,7 @@
 cat("\n\n")
 
 #saving R data in .Rdata file to save the variables used in the present tool
-objects2save = c("xdata","zipfile","singlefile","md5sumList","sampleNamesList", "chromTIC", "chromBPI", "chromTIC_adjusted", "chromBPI_adjusted")
+objects2save = c("xdata","zipfile","singlefile","md5sumList","sampleNamesList") #, "chromTIC", "chromBPI", "chromTIC_adjusted", "chromBPI_adjusted")
 save(list=objects2save[objects2save %in% ls()], file="fillpeaks.RData")
 
 cat("\n\n")