Update docs

man/p.sw.Rd

@@ -4,10 +4,13 @@
 \alias{p.sw}
 \title{Parallel Spectral Workflow.}
 \usage{
-p.sw(fn_data, stgs_alist, wd, fn_cmpd_list, mode, readMethod = "mzR",
-  archdir = "archive", lastStep = 8, combine = F, cl = NULL)
+p.sw(cl, fn_data, stgs_alist, wd, fn_cmpd_list, mode, readMethod = "mzR",
+  archdir = "archive", lastStep = 8, combine = F,
+  combdest = "combined")
 }
 \arguments{
+\item{cl}{Cluster.}
+
 \item{fn_data}{A sequence of mzML input files.}
 
 \item{stgs_alist}{A list of named list of settings, or a list of
@@ -28,7 +31,7 @@ filenames of YAML files containing the settings.}
 \item{combine}{If TRUE, use combineMultiplicies to merge
 workspaces corresponding to different collisional energies.}
 
-\item{cl}{Cluster.}
+\item{combdest}{Combine destination directory.}
 }
 \value{
 A named list of spectral workspaces. The names are derived

man/sw.do.Rd

@@ -4,7 +4,7 @@
 \alias{sw.do}
 \title{Perform MassBank Workflow on Multiple Compound Mixtures}
 \usage{
-sw.do(fn_data, fn_cmpd_list, mode, rdir = ".", combine = F, proc = F)
+sw.do(fn_data, fn_cmpd_list, mode, dest = ".", combine = F, proc = F)
 }
 \arguments{
 \item{fn_data}{List of mzML data filenames to be processed.}
@@ -13,7 +13,7 @@ sw.do(fn_data, fn_cmpd_list, mode, rdir = ".", combine = F, proc = F)
 
 \item{mode}{as in msmsRead.}
 
-\item{rdir}{The root data directory.}
+\item{dest}{The destination data directory.}
 
 \item{combine}{If TRUE, use combineMultiplicies to merge
 workspaces corresponding to different collisional energies.}

man/sw.single.1.Rd

+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/mix.R
+\name{sw.single.1}
+\alias{sw.single.1}
+\title{RMassBank Spectral Workflow on a Single Compound Mixture (step 1)}
+\usage{
+sw.single.1(fn_data, stgs_alist, wd, fn_cmpd_list, mode,
+  readMethod = "mzR")
+}
+\arguments{
+\item{fn_data}{A mzML data file.}
+
+\item{stgs_alist}{RMassBank settings. It can either be a named
+list of settings, or a filename of a YAML file.}
+
+\item{wd}{The name of the work directory.}
+
+\item{fn_cmpd_list}{The file name of he compound list
+corresponding to \code{fn_data}.}
+
+\item{mode}{Modes as described in the standard workflow vignette
+of RMassBank.}
+
+\item{readMethod}{Default read method is "mzR". Consult the
+documentation of \code{msmsRead} for details.}
+}
+\value{
+MsmsWorkspace object.
+}
+\description{
+Runs the first step of the compound mixture workflow on a single mzML file.
+}
+\author{
+Todor Kondić
+}

man/single.sw.Rd → man/sw.single.Rd

 % Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/mix.R
-\name{single.sw}
-\alias{single.sw}
+\name{sw.single}
+\alias{sw.single}
 \title{RMassBank Spectral Workflow on a Single Compound Mixture}
 \usage{
-single.sw(fn_data, stgs_alist, wd, fn_cmpd_list, mode,
+sw.single(fn_data, stgs_alist, wd, fn_cmpd_list, mode,
   readMethod = "mzR", archdir = "archive", lastStep = 8)
 }
 \arguments{

man/sw.single.next.Rd

+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/mix.R
+\name{sw.single.next}
+\alias{sw.single.next}
+\title{RMassBank Spectral Workflow on a Single Compound Mixture (after step 1)}
+\usage{
+sw.single.next(w, wd, archdir = "archive", lastStep = 8)
+}
+\arguments{
+\item{w}{The msmsWorkspace object that was processed by
+sw.single.1.}
+
+\item{wd}{The current working dir.}
+
+\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.
+}
+\description{
+Runs steps after sw.single.1 of compound mixture workflow on a
+single mzML file.
+}
+\author{
+Todor Kondić
+}