Update single.sw in R/mix.R

* R/mix.R(single.sw): New argument.
  [lastStep] Controls at which point to finish spectral step.

* man/single.sw.Rd: Update documentation.

R/mix.R

@@ -117,7 +117,7 @@ single.sw<-function(fn_data,stgs_alist,wd,fn_cmpd_list,mode,readMethod="mzR",arc
     archdir<-file.path(wd,archdir)
     if (!dir.exists(archdir)) dir.create(archdir)
     fn_arch<-file.path(archdir,paste(fn_data,".archive",sep=''))
-    RMassBank::msmsWorkflow(w, mode=mode, steps=2:8,archivename=fn_arch)
+    RMassBank::msmsWorkflow(w, mode=mode, steps=2:lastStep,archivename=fn_arch)
 }
 
 

man/single.sw.Rd

@@ -5,7 +5,7 @@
 \title{RMassBank Spectral Workflow on a Single Compound Mixture}
 \usage{
 single.sw(fn_data, stgs_alist, wd, fn_cmpd_list, mode,
-  readMethod = "mzR", archdir = "archive")
+  readMethod = "mzR", archdir = "archive", lastStep = 8)
 }
 \arguments{
 \item{fn_data}{A mzML data file.}
@@ -26,6 +26,8 @@ documentation of \code{msmsRead} for details.}
 
 \item{archdir}{The directory to store R objects created during
 workflow execution.}
+
+\item{lastStep}{The last step in the workflow. Default is eight.}
 }
 \value{
 MsmsWorkspace object.