Merge pull request #705 from ARTbio/gsc_center_scale

update gsc_center_scale

tools/gsc_center_scale/.shed.yml

@@ -7,6 +7,7 @@ long_description: |
   transcriptomic data, or any type of numerical data
 categories:
   - Statistics
+  - Single Cell
 homepage_url: http://artbio.fr
 remote_repository_url: https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_center_scale
 toolshed:

tools/gsc_center_scale/center_scale.R

@@ -1,95 +1,101 @@
-options(show.error.messages = FALSE,
-  error = function() {
-    cat(geterrmessage(), file = stderr())
-    q("no", 1, FALSE)
-  }
+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(
-  make_option(
-    "--data",
-    default = NA,
-    type = "character",
-    help = "Input file that contains values to transform. Must be tabular separated,
+    make_option(
+        "--data",
+        default = NA,
+        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",
-    default = TRUE,
-    type = "logical",
-    help = "center data to the mean [default : '%default' ]"
-  ),
-  make_option(
-    "--scale",
-    default = TRUE,
-    type = "logical",
-    help = "scale data to standard deviation [default : '%default' ]"
-  ),
-  make_option(
-    "--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",
-    help = "Table of transformed values [default : '%default' ]"
-  )
+    ),
+    make_option(
+        "--center",
+        default = TRUE,
+        type = "logical",
+        help = "center data to the mean [default : '%default' ]"
+    ),
+    make_option(
+        "--scale",
+        default = TRUE,
+        type = "logical",
+        help = "scale data to standard deviation [default : '%default' ]"
+    ),
+    make_option(
+        "--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",
+        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)))
+    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))
+    args = commandArgs(trailingOnly = TRUE)
+)
 
 data <- read.delim(
-  opt$data,
-  check.names = FALSE,
-  header = TRUE,
-  row.names = 1,
-  sep = "\t"
+    opt$data,
+    check.names = FALSE,
+    header = TRUE,
+    row.names = 1,
+    sep = "\t"
 )
 
 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)
-  }
+    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),
-  opt$output,
-  col.names = TRUE,
-  row.names = FALSE,
-  quote = FALSE,
-  sep = "\t"
+    cbind(gene = rownames(data_transformed), data_transformed),
+    opt$output,
+    col.names = TRUE,
+    row.names = FALSE,
+    quote = FALSE,
+    sep = "\t"
 )

tools/gsc_center_scale/center_scale.xml

@@ -1,5 +1,8 @@
-<tool id="center_scale" name="Center or scale (standardize) data" version="4.3.1+galaxy0" profile="21.01">
+<tool id="center_scale" name="Center or scale (standardize) data" version="4.3.1+galaxy1" profile="21.01">
     <description></description>
+    <xrefs>
+        <xref type="bio.tools">galaxy_single_cell_suite</xref>
+    </xrefs>
     <requirements>
         <requirement type="package" version="1.7.3">r-optparse</requirement>
     </requirements>