Merge pull request #35 from martinghunt/summary_help_tweak

Clarify usage: input must be tsv, not xls

ariba/tasks/summary.py

@@ -4,9 +4,9 @@
 def run():
     parser = argparse.ArgumentParser(
         description = 'Make a summry of ARIBA report files',
-        usage = 'ariba summary [options] <outfile> [infiles]',
-        epilog = 'Files must be listed after the output file and/or the option --fofn must be used. If both used, all files in the filename specified by --fofn AND the files listed after the output file will be used as input')
-    parser.add_argument('-f', '--fofn', help='File of filenames of ariba reports to be summarised. Must b used if no input files listed after the outfile', metavar='FILENAME')
+        usage = 'ariba summary [options] <outfile> [report1.tsv report2.tsv ...]',
+        epilog = 'Files must be listed after the output file and/or the option --fofn must be used. If both used, all files in the filename specified by --fofn AND the files listed after the output file will be used as input. The input report files must be in tsv format, not xls.')
+    parser.add_argument('-f', '--fofn', help='File of filenames of ariba reports in tsv format (not xls) to be summarised. Must be used if no input files listed after the outfile.', metavar='FILENAME')
     parser.add_argument('--min_id', type=float, help='Minimum percent identity cutoff to count as assembled [%(default)s]', default=90, metavar='FLOAT')
     parser.add_argument('outfile', help='Name of output file. If file ends with ".xls", then an excel spreadsheet is written. Otherwise a tsv file is written')
     parser.add_argument('infiles', nargs='*', help='Files to be summarised')
@@ -19,5 +19,5 @@ def run():
         fofn=options.fofn,
         filenames=options.infiles,
         min_id=options.min_id
-    ) 
+    )
     s.run()