Mercurial > repos > greg > ideas_preprocessor
changeset 18:504226a7eb75 draft
Uploaded
| author | greg |
|---|---|
| date | Tue, 30 Jan 2018 13:21:00 -0500 |
| parents | 6ff92012abb7 |
| children | c7e0b4358961 |
| files | ideas_preprocessor.R |
| diffstat | 1 files changed, 3 insertions(+), 4 deletions(-) [+] |
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--- 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$options -create_primary_html = function(output, output_hid, output_files_path) { +create_primary_html = function(output, output_files_path) { files = list.files(path=output_files_path); s <- paste('<html><head></head><body>', sep="\n"); - s <- paste(s, '<h3>History item ', output_hid, ' files prepared for IDEAS</h3>\n', sep=""); + s <- paste(s, '<h3>Files prepared for IDEAS</h3>\n', sep=""); s <- paste(s, '<ul>\n', sep=""); for (i in 1:length(files)) { s <- paste(s, '<li><a href="', files[i], '">', files[i], '</a></li>\n', sep=""); @@ -117,4 +116,4 @@ file.rename(opt$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);