fix: read chemstation .ms files with entab

NEWS.md

@@ -1,6 +1,7 @@
 ## chromConverter 0.6.0
 
 * Added parser for reading ANDI MS (`.cdf`) files.
+* Fixed parsing of Agilent MS files with 'entab' reader.
 * Fixed `read_chemstation_ch` parser to correctly read "Mustang Chemstation" 179 files with 8-byte encoding.
 * Added alias to `read_chroms` for reading `mzxml` files with `RaMS`.
 * Added internal parser for 1D 'Waters RAW' chromatograms.

R/call_entab.R

@@ -28,17 +28,24 @@ call_entab <- function(file, data_format = c("wide", "long"),
   metadata_format <- switch(metadata_format,
                             chromconverter = format_in, raw = "raw")
   r <- entab::Reader(file)
-  x <- entab::as.data.frame(r)
-  signal.idx <- grep("signal", colnames(x))
-  if (length(signal.idx) == 1){
-    colnames(x)[signal.idx] <- "wavelength"
+  if (is.null(format_in)){
+    format_in <- r$parser()
   }
-  if (data_format == "wide"){
+  x <- entab::as.data.frame(r)
+  if (format_in == "chemstation_uv"){
+    signal.idx <- grep("signal", colnames(x))
+    if (length(signal.idx) == 1){
+      colnames(x)[signal.idx] <- "wavelength"
+    }
+    if (data_format == "wide"){
       x <- reshape_chrom_wide(x, time_var = "time", lambda_var = "wavelength",
                               value_var = "intensity")
-  }
-  if (format_out == "matrix"){
-    x <- as.matrix(x)
+      if (format_out == "matrix"){
+        x <- as.matrix(x)
+      }
+    }
+  } else if (format_in == "chemstation_ms"){
+    colnames(x)[1] <- "rt"
   }
   if (read_metadata){
     meta <- r$metadata()