# HG changeset patch
# User greg
# Date 1517336460 18000
# Node ID 504226a7eb75d3a8eca4efd022e187e0cd10d12d
# Parent 6ff92012abb79c94bbfa1dce90d9fe04df48f435
Uploaded
diff -r 6ff92012abb7 -r 504226a7eb75 ideas_preprocessor.R
--- a/ideas_preprocessor.R Tue Jan 30 13:20:01 2018 -0500
+++ b/ideas_preprocessor.R Tue Jan 30 13:21:00 2018 -0500
@@ -22,7 +22,6 @@
make_option(c("--ideaspre_input_config"), action="store", dest="ideaspre_input_config", help="Preprocessing input config file"),
make_option(c("--output"), action="store", dest="output", help="Primary output dataset"),
make_option(c("--output_files_path"), action="store", dest="output_files_path", help="Primary output dataset extra files path"),
- make_option(c("--output_hid"), action="store", dest="output_hid", help="Primary output dataset hid"),
make_option(c("--reads_per_bp"), action="store", dest="reads_per_bp", type="integer", help="Calculate the signal in each genomic window"),
make_option(c("--restrict_to_chroms"), action="store", dest="restrict_to_chroms", default=NULL, help="Restrict processing to specified chromosomes"),
make_option(c("--standardize_datasets"), action="store_true", dest="standardize_datasets", default=FALSE, help="Standardize all datasets"),
@@ -34,10 +33,10 @@
args <- parse_args(parser, positional_arguments=TRUE)
opt <- args$options
-create_primary_html = function(output, output_hid, output_files_path) {
+create_primary_html = function(output, output_files_path) {
files = list.files(path=output_files_path);
s <- paste('', sep="\n");
- s <- paste(s, 'History item ', output_hid, ' files prepared for IDEAS
\n', sep="");
+ s <- paste(s, 'Files prepared for IDEAS
\n', sep="");
s <- paste(s, '\n', sep="");
for (i in 1:length(files)) {
s <- paste(s, '- ', files[i], '
\n', sep="");
@@ -117,4 +116,4 @@
file.rename(opt$chromosome_windows, to_path);
}
# Create the primary HTML dataset.
-create_primary_html(opt$output, opt$output_hid, opt$output_files_path);
+create_primary_html(opt$output, opt$output_files_path);