diff read2mut.py @ 12:7a418148319d draft

planemo upload for repository https://github.com/Single-Molecule-Genetics/VariantAnalyzerGalaxy/tree/master/tools/variant_analyzer commit ee4a8e6cf290e6c8a4d55f9cd2839d60ab3b11c8

--- a/read2mut.py	Mon Feb 15 21:53:24 2021 +0000
+++ b/read2mut.py	Tue Feb 16 07:08:25 2021 +0000
@@ -46,7 +46,11 @@
     parser.add_argument('--sscsJson',
                         help='JSON file with SSCS counts collected by mut2sscs.py.')
     parser.add_argument('--outputFile',
-                        help='Output xlsx file of mutation details.')
+                        help='Output xlsx file with summary of mutations.')
+    parser.add_argument('--outputFile2',
+                        help='Output xlsx file with allele frequencies of mutations.')
+    parser.add_argument('--outputFile3',
+                        help='Output xlsx file with examples of the tier classification.')
     parser.add_argument('--thresh', type=int, default=0,
                         help='Integer threshold for displaying mutations. Only mutations occuring less than thresh times are displayed. Default of 0 displays all.')
     parser.add_argument('--phred', type=int, default=20,
@@ -72,6 +76,8 @@
     json_file = args.inputJson
     sscs_json = args.sscsJson
     outfile = args.outputFile
+    outfile2 = args.outputFile2
+    outfile3 = args.outputFile3
     thresh = args.thresh
     phred_score = args.phred
     trim = args.trim