--- a/center_scale.R	Fri Jul 12 11:44:50 2019 -0400
+++ b/center_scale.R	Sun Oct 15 16:16:16 2023 +0000
@@ -1,103 +1,95 @@
-options( show.error.messages=F,
-       error = function () { cat( geterrmessage(), file=stderr() ); q( "no", 1, F ) } )
+options(show.error.messages = FALSE,
+  error = function() {
+    cat(geterrmessage(), file = stderr())
+    q("no", 1, FALSE)
+  }
+)
 loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")
 warnings()
 library(optparse)
 
 # Arguments
-option_list = list(
+option_list <- list(
   make_option(
-    '--data',
+    "--data",
     default = NA,
-    type = 'character',
+    type = "character",
     help = "Input file that contains values to transform. Must be tabular separated,
             with columns and row names, variables in rows, observations in columns  [default : '%default' ]"
   ),
   make_option(
-   '--center',
+    "--center",
     default = TRUE,
-    type = 'logical',
+    type = "logical",
     help = "center data to the mean [default : '%default' ]"
   ),
   make_option(
-   '--scale',
+    "--scale",
     default = TRUE,
-    type = 'logical',
+    type = "logical",
     help = "scale data to standard deviation [default : '%default' ]"
   ),
   make_option(
-    '--factor',
-    default = '',
-    type = 'character',
+    "--factor",
+    default = "",
+    type = "character",
     help = "A two-column observations|factor_levels table, to group observations to be transformed by levels  [default : '%default' ]"
   ),
   make_option(
-    '--output',
-    default = 'res.tab',
-    type = 'character',
+    "--output",
+    default = "res.tab",
+    type = "character",
     help = "Table of transformed values [default : '%default' ]"
   )
 )
 
-transform <- function(df, center=TRUE, scale=TRUE) {
-    transfo <- scale(
-        t(df),
-        center=center,
-        scale=scale
-        )
-    return(as.data.frame(t(transfo)))
+transform <- function(df, center = TRUE, scale = TRUE) {
+  transfo <- scale(t(df),
+    center = center,
+    scale = scale
+  )
+  return(as.data.frame(t(transfo)))
 }
 
-opt = parse_args(OptionParser(option_list = option_list),
-                 args = commandArgs(trailingOnly = TRUE))
+opt <- parse_args(OptionParser(option_list = option_list),
+                  args = commandArgs(trailingOnly = TRUE))
 
-data = read.table(
-    opt$data,
-    check.names = FALSE,
-    header = TRUE,
-    row.names = 1,
-    sep = '\t'
+data <- read.delim(
+  opt$data,
+  check.names = FALSE,
+  header = TRUE,
+  row.names = 1,
+  sep = "\t"
 )
 
-if (opt$factor != '') {
-    data.factor = read.table(
-        opt$factor,
-        check.names = FALSE,
-        header = TRUE,
-        sep = '\t'
-        )
-    colnames(data.factor) <- c("cellid", "level")
-    data.transformed <- data.frame(row.names=rownames(data), stringsAsFactors=FALSE)
-    for (group in levels(data.factor$level)){
-        subcells <- as.data.frame(subset(data.factor, level==group, select=cellid))
-        subdata <- as.data.frame(subset(data, select=as.vector(subcells$cellid)))
-        subdata.transformed <- transform(subdata, center=as.logical(opt$center),
-                                                  scale=as.logical(opt$scale))
-        data.transformed <- cbind(data.transformed, subdata.transformed)
-    }
+if (opt$factor != "") {
+  data_factor <- read.delim(
+    opt$factor,
+    check.names = FALSE,
+    header = TRUE,
+    sep = "\t",
+    stringsAsFactors = TRUE
+  )
+  colnames(data_factor) <- c("cellid", "level")
+  data_transformed <- data.frame(row.names = rownames(data))
+  for (group in levels(data_factor$level)) {
+    subcells <- as.data.frame(subset(data_factor, level == group, select = cellid))
+    subdata <- as.data.frame(subset(data, select = as.vector(subcells$cellid)))
+    subdata_transformed <- transform(subdata, center = as.logical(opt$center),
+                                     scale = as.logical(opt$scale))
+    data_transformed <- cbind(data_transformed, subdata_transformed)
+  }
 } else {
-    data.transformed <- transform(data, center=as.logical(opt$center),
-                                        scale=as.logical(opt$scale))
+  data_transformed <- transform(data, center = as.logical(opt$center),
+                                scale = as.logical(opt$scale))
 }
 
 
 write.table(
-  cbind(gene=rownames(data.transformed), data.transformed),
+  cbind(gene = rownames(data_transformed), data_transformed),
   opt$output,
   col.names = TRUE,
   row.names = FALSE,
-  quote = F,
+  quote = FALSE,
   sep = "\t"
 )
-
-
-
-
-
-
-
-
-
-
-
-

--- a/center_scale.xml	Fri Jul 12 11:44:50 2019 -0400
+++ b/center_scale.xml	Sun Oct 15 16:16:16 2023 +0000
@@ -1,7 +1,7 @@
-<tool id="center_scale" name="Center or scale (standardize) data" version="0.9.5">
+<tool id="center_scale" name="Center or scale (standardize) data" version="4.3.1+galaxy0" profile="21.01">
     <description></description>
     <requirements>
-        <requirement type="package" version="1.6.0">r-optparse</requirement>
+        <requirement type="package" version="1.7.3">r-optparse</requirement>
     </requirements>
     <stdio>
         <exit_code range="1:" level="fatal" description="Tool exception" />
@@ -94,7 +94,7 @@
 The tool perform various normalization operations on a data table, including mean centering,
 standard deviation rescaling, or both (standardization).
 
-In addition, these operations can be performed on subsets of observations, is the user provides
+In addition, these operations can be performed on subsets of observations, if the user provides
 a two-column table that maps observations to groups (factor levels).
 
 **Inputs**