--- a/ideas_preprocessor.R	Wed Jan 24 10:16:04 2018 -0500
+++ b/ideas_preprocessor.R	Wed Jan 24 10:16:11 2018 -0500
@@ -1,10 +1,11 @@
+(.venv) [galaxy@IDEAS ideas_preprocessor]$ cat ideas_preprocessor.R
 #!/usr/bin/env Rscript
 
 suppressPackageStartupMessages(library("data.table"))
 suppressPackageStartupMessages(library("optparse"))
 
 option_list <- list(
-        make_option(c("--chrom_bed_input"), action="store", dest="chrom_bed_input", defaul=NULL, help="Chromosome windows positions file"),
+        make_option(c("--bed_input"), action="store", dest="bed_input", defaul=NULL, help="Chromosome windows positions file"),
         make_option(c("--exclude_input"), action="store", dest="exclude_input", defaul=NULL, help="File(s) containing regions to exclude"),
         make_option(c("--bychr"), action="store_true", dest="bychr", defaul=FALSE, help="Separate files by chromosome"),
         make_option(c("--chrom_len_file"), action="store", dest="chrom_len_file", default=NULL, help="Chromosome lengths file"),
@@ -59,27 +60,27 @@
     }
     bed_file_name = paste(file_name, "bed", sep=".");
     bed_file_path = paste("tmp", bed_file_name, sep="/");
-    cmd = paste("bigWigAverageOverBed", bigwig_file_name, opt$chrom_bed_input, "stdout | cut -f5 >", bed_file_path);
+    cmd = paste("bigWigAverageOverBed", bigwig_file_name, opt$bed_input, "stdout | cut -f5 >", bed_file_path);
     system(cmd);
     cmd = paste("gzip -f", bed_file_path);
     system(cmd);
 }
 
-# Create temporary file1.txt.
+# Create file1.txt.
 cmd = paste("cut -d' '", opt$ideaspre_input_config, "-f1,2 > file1.txt", sep=" ");
 system(cmd);
 # Compress the bed files in the tmp directory.
 tmp_gzipped_files = paste(tmp_dir, "*.bed.gz", sep="/");
-# Create temporary file2.txt.
+# Create file2.txt.
 cmd = paste("ls", tmp_gzipped_files, "> file2.txt", sep=" ");
 system(cmd);
-# Create IDEAS_input_config.txt with the format required by IDEAS.
+# Create the ideas_input_config with the format required by IDEAS.
 cmd = paste("paste -d' ' file1.txt file2.txt >", opt$ideas_input_config, sep=" ");
 system(cmd);
-# Move IDEAS_input_config.txt to the output directory.
+# Move the ideas_input_config to the output directory.
 to_path = paste(opt$output_files_path, opt$ideas_input_config, sep="/");
 file.rename(opt$ideas_input_config, to_path);
-# Move all compressed bed files in the tmp
+# Move the compressed bed files in the tmp
 # directory to the output tmp directory.
 tmp_files = list.files(path=tmp_dir);
 for (i in 1:length(tmp_files)) {
@@ -87,14 +88,10 @@
     to_path = paste(output_tmp_dir, tmp_files[i], sep="/");
     file.rename(from_path, to_path);
 }
-if (!is.null(opt$chrom_bed_input) && !is.null(opt$chromosome_windows)) {
-    # Rename chrom_bed_input to chromosomes.txt
-    # and move it to the output directory.
-    to_path = paste(opt$output_files_path, "chromosomes.bed", sep="/");
-    file.rename(opt$chrom_bed_input, to_path)
-    # Move chromosome_windows.txt to the output directory.
+if (!is.null(opt$chromosome_windows)) {
+    # Move the chromosome_windows to the output directory.
     to_path = paste(opt$output_files_path, opt$chromosome_windows, sep="/");
     file.rename(opt$chromosome_windows, to_path);
 }
 # Create the primary HTML dataset.
-create_primary_html(opt$output, opt$output_hid, opt$output_files_path);
\ No newline at end of file
+create_primary_html(opt$output, opt$output_hid, opt$output_files_path);