# HG changeset patch
# User iuc
# Date 1594276717 14400
# Node ID b833eff63b10c6594503658172632a2ba2ee6e54
# Parent  25abc2c72ff96fb3ccf984cb97d9c0192b563456
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit c2985b5c91a932e175cbfaf9b54a76e23beff9e9"

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
@@ -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)
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
@@ -1,2 +0,0 @@
-chr	22104	22105	0.5940708247528699
-chr	22105	22106	0.5940708247528699