Previous changeset 2:25abc2c72ff9 (2020-06-17) Next changeset 4:c0fb573c1e8d (2022-06-23) |
Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit c2985b5c91a932e175cbfaf9b54a76e23beff9e9" |
modified:
NanocomporeDB_process.py |
removed:
test-data/KS_intensity_pvalue.bedgraph |
b |
diff -r 25abc2c72ff9 -r b833eff63b10 NanocomporeDB_process.py --- a/NanocomporeDB_process.py Wed Jun 17 13:28:27 2020 -0400 +++ b/NanocomporeDB_process.py Thu Jul 09 02:38:37 2020 -0400 |
b |
@@ -40,7 +40,7 @@ help='path to the annotations') parser.add_argument('--bedgraph', action="store_true", help='write output in BEDGRAPH format instead of BED') - parser.add_argument('--pvalue-threshold', default=1.0, + parser.add_argument('--pvalue-threshold', type=float, default=1.0, help='Maximum reported p-value.') parser.add_argument('--out-dir', default="./", type=is_valid_directory, help='path the plotting output directory.') @@ -52,9 +52,15 @@ print(db) print("DB read ids:", db.ref_id_list) + if args.bedgraph: + file_ext = 'bedgraph' + else: + file_ext = 'bed' + if args.annotation_bed: for pt in args.pvalue_types.split(','): - print("bedgraph output for p-value type:", pt) - db.save_to_bed(output_fn='{}/{}.bedgraph'.format(args.out_dir, pt), + out_path = '{}/{}.{}'.format(args.out_dir, pt, file_ext) + print("%s output for p-value type:" % out_path, pt) + db.save_to_bed(output_fn=out_path, pvalue_field=pt, pvalue_thr=args.pvalue_threshold, bedgraph=args.bedgraph) |
b |
diff -r 25abc2c72ff9 -r b833eff63b10 test-data/KS_intensity_pvalue.bedgraph --- a/test-data/KS_intensity_pvalue.bedgraph Wed Jun 17 13:28:27 2020 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
b |
@@ -1,2 +0,0 @@ -chr 22104 22105 0.5940708247528699 -chr 22105 22106 0.5940708247528699 |