diff --git a/tools/xcms/macros_xcms.xml b/tools/xcms/macros_xcms.xml
index 83540af00..382e8fbf2 100644
--- a/tools/xcms/macros_xcms.xml
+++ b/tools/xcms/macros_xcms.xml
@@ -2,7 +2,7 @@
 <macros>
 
     <token name="@TOOL_VERSION@">3.12.0</token>
-    <token name="@VERSION_SUFFIX@">3</token>
+    <token name="@VERSION_SUFFIX@">4</token>
     <token name="@PROFILE@">21.09</token>
     <xml name="requirements">
         <requirements>
diff --git a/tools/xcms/xcms_fillpeaks.r b/tools/xcms/xcms_fillpeaks.r
index 6ae401e0e..60e414637 100755
--- a/tools/xcms/xcms_fillpeaks.r
+++ b/tools/xcms/xcms_fillpeaks.r
@@ -57,9 +57,14 @@ if (!hasFeatures(xdata)) stop("You must always do a group step after a retcor. O
 # Handle infiles
 if (!exists("singlefile")) singlefile <- NULL
 if (!exists("zipfile")) zipfile <- NULL
-rawFilePath <- retrieveRawfileInTheWorkingDir(singlefile, zipfile, args)
-zipfile <- rawFilePath$zipfile
-singlefile <- rawFilePath$singlefile
+
+# Handle infiles
+rawFilePath <- retrieveRawfileInTheWorkingDir(NULL, NULL, args)
+# zipfile <- rawFilePath$zipfile
+# singlefile <- rawFilePath$singlefile
+
+force(singlefile)
+force(zipfile)
 
 
 cat("\n\n")
diff --git a/tools/xcms/xcms_group.r b/tools/xcms/xcms_group.r
index de01ba83e..7e13bc3c7 100755
--- a/tools/xcms/xcms_group.r
+++ b/tools/xcms/xcms_group.r
@@ -54,9 +54,14 @@ if (!exists("xdata")) stop("\n\nERROR: The RData doesn't contain any object call
 # Handle infiles
 if (!exists("singlefile")) singlefile <- NULL
 if (!exists("zipfile")) zipfile <- NULL
-rawFilePath <- retrieveRawfileInTheWorkingDir(singlefile, zipfile, args)
-zipfile <- rawFilePath$zipfile
-singlefile <- rawFilePath$singlefile
+
+# Handle infiles
+rawFilePath <- retrieveRawfileInTheWorkingDir(NULL, NULL, args)
+# zipfile <- rawFilePath$zipfile
+# singlefile <- rawFilePath$singlefile
+
+force(singlefile)
+force(zipfile)
 
 cat("\n\n")
 
diff --git a/tools/xcms/xcms_refine.r b/tools/xcms/xcms_refine.r
index ad04f90e6..9cc10bfa9 100755
--- a/tools/xcms/xcms_refine.r
+++ b/tools/xcms/xcms_refine.r
@@ -64,9 +64,14 @@ if (!exists("xdata")) stop("\n\nERROR: The RData doesn't contain any object call
 # Handle infiles
 if (!exists("singlefile")) singlefile <- NULL
 if (!exists("zipfile")) zipfile <- NULL
-rawFilePath <- retrieveRawfileInTheWorkingDir(singlefile, zipfile, args)
-zipfile <- rawFilePath$zipfile
-singlefile <- rawFilePath$singlefile
+
+# Handle infiles
+rawFilePath <- retrieveRawfileInTheWorkingDir(NULL, NULL, args)
+# zipfile <- rawFilePath$zipfile
+# singlefile <- rawFilePath$singlefile
+
+force(singlefile)
+force(zipfile)
 
 cat("\n\n")
 
diff --git a/tools/xcms/xcms_retcor.r b/tools/xcms/xcms_retcor.r
index f7ce84b63..e7e97c296 100755
--- a/tools/xcms/xcms_retcor.r
+++ b/tools/xcms/xcms_retcor.r
@@ -49,9 +49,15 @@ if (!exists("xdata")) stop("\n\nERROR: The RData doesn't contain any object call
 # Handle infiles
 if (!exists("singlefile")) singlefile <- NULL
 if (!exists("zipfile")) zipfile <- NULL
-rawFilePath <- retrieveRawfileInTheWorkingDir(singlefile, zipfile, args)
-zipfile <- rawFilePath$zipfile
-singlefile <- rawFilePath$singlefile
+
+# Handle infiles
+rawFilePath <- retrieveRawfileInTheWorkingDir(NULL, NULL, args)
+# zipfile <- rawFilePath$zipfile
+# singlefile <- rawFilePath$singlefile
+
+force(singlefile)
+force(zipfile)
+
 
 cat("\n\n")
 
diff --git a/tools/xcms/xcms_xcmsSet.r b/tools/xcms/xcms_xcmsSet.r
index 4e654f11a..0622ebe9f 100755
--- a/tools/xcms/xcms_xcmsSet.r
+++ b/tools/xcms/xcms_xcmsSet.r
@@ -64,9 +64,14 @@ load(args$image)
 if (!exists("raw_data")) stop("\n\nERROR: The RData doesn't contain any object called 'raw_data' which is provided by the tool: MSnbase readMSData")
 
 # Handle infiles
-rawFilePath <- retrieveRawfileInTheWorkingDir(singlefile, zipfile, args)
-zipfile <- rawFilePath$zipfile
-singlefile <- rawFilePath$singlefile
+rawFilePath <- retrieveRawfileInTheWorkingDir(NULL, NULL, args)
+# zipfile <- rawFilePath$zipfile
+# singlefile <- rawFilePath$singlefile
+
+# force(args)
+force(singlefile)
+force(zipfile)
+# force(raw_data)
 
 
 cat("\n\n")