Checks added in case of singlefile NULL

workflow4metabolomics · Oct 25, 2024 · d83c1f0 · d83c1f0
1 parent d078329
commit d83c1f0
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Showing 4 changed files with 20 additions and 4 deletions.
diff --git a/tools/camera/CAMERA_findAdducts.R b/tools/camera/CAMERA_findAdducts.R
@@ -50,7 +50,11 @@ rawFilePath <- getRawfilePathFromArguments(singlefile, zipfile, args)
 zipfile <- rawFilePath$zipfile
 singlefile <- rawFilePath$singlefile
 args <- rawFilePath$args
-directory <- retrieveRawfileInTheWorkingDir(singlefile, zipfile)
+
+print("singlefile :", singlefile)
+if (!is.null(singlefile)) {
+  directory <- retrieveRawfileInTheWorkingDir(singlefile, zipfile)
+}
 
 # Check if the 'rules' argument in 'args' is NULL
 if (is.null(args$rules)) {

diff --git a/tools/camera/CAMERA_findIsotopes.R b/tools/camera/CAMERA_findIsotopes.R
@@ -50,7 +50,11 @@ rawFilePath <- getRawfilePathFromArguments(singlefile, zipfile, args)
 zipfile <- rawFilePath$zipfile
 singlefile <- rawFilePath$singlefile
 args <- rawFilePath$args
-directory <- retrieveRawfileInTheWorkingDir(singlefile, zipfile)
+
+print("singlefile :", singlefile)
+if (!is.null(singlefile)) {
+  directory <- retrieveRawfileInTheWorkingDir(singlefile, zipfile)
+}
 
 # Verify if the xa object is loaded
 if (!exists("xa")) {

diff --git a/tools/camera/CAMERA_groupCorr.R b/tools/camera/CAMERA_groupCorr.R
@@ -50,7 +50,11 @@ rawFilePath <- getRawfilePathFromArguments(singlefile, zipfile, args)
 zipfile <- rawFilePath$zipfile
 singlefile <- rawFilePath$singlefile
 args <- rawFilePath$args
-directory <- retrieveRawfileInTheWorkingDir(singlefile, zipfile)
+
+print("singlefile :", singlefile)
+if (!is.null(singlefile)) {
+  directory <- retrieveRawfileInTheWorkingDir(singlefile, zipfile)
+}
 
 # Ensure the xa object is loaded
 if (!exists("xa")) {

diff --git a/tools/camera/CAMERA_groupFWHM.R b/tools/camera/CAMERA_groupFWHM.R
@@ -50,7 +50,11 @@ rawFilePath <- getRawfilePathFromArguments(singlefile, zipfile, args)
 zipfile <- rawFilePath$zipfile
 singlefile <- rawFilePath$singlefile
 args <- rawFilePath$args
-directory <- retrieveRawfileInTheWorkingDir(singlefile, zipfile)
+
+print("singlefile :", singlefile)
+if (!is.null(singlefile)) {
+  directory <- retrieveRawfileInTheWorkingDir(singlefile, zipfile)
+}
 
 # If the xdata object exists, convert it to xcmsSet
 if (exists("xdata")) {