56e1d09dbeac2c8233ef0ca36541e937a068c8aa
ceisenhart
  Fri May 12 10:30:32 2017 -0700
Fixing up the usage statement, refs #19155

diff --git src/utils/expMatrixToBarchartBed/expMatrixToBarchartBed src/utils/expMatrixToBarchartBed/expMatrixToBarchartBed
index 3e155c2..53e18f3 100755
--- src/utils/expMatrixToBarchartBed/expMatrixToBarchartBed
+++ src/utils/expMatrixToBarchartBed/expMatrixToBarchartBed
@@ -11,32 +11,33 @@
 def parseArgs(args):
     """
     Parse the command line arguments.
     """
     parser= argparse.ArgumentParser(description = __doc__)
     parser.add_argument ("sampleFile",
         help = " Two column no header, the first column is the samples which should match " + \
                 "the matrix, the second is the grouping (cell type, tissue, etc)",
         type = argparse.FileType("r"))
     parser.add_argument ("matrixFile",
             help = " The input matrix file. The samples in the first row should exactly match the ones in " + \
                 "the sampleFile. The labels (ex ENST*****) in the first column should exactly match " + \
                 "the ones in the bed file.",
         type = argparse.FileType("r"))
     parser.add_argument ("bedFile",
-        help = " Bed4+2 format. File that maps the column labels from the matrix to coordinates. Tab " + \
-                "separated; chr, start coord, end coord, label, strand, gene name. ",
+        help = " Bed6+1 format. File that maps the column labels from the matrix to coordinates. Tab " + \
+                "separated; chr, start coord, end coord, label, score, strand, gene name. The score " + \
+                "column is ignored.",
         action = "store")
     parser.add_argument ("outputFile",
         help = " The output file, bed 6+5 format. See the schema in kent/src/hg/lib/barChartBed.as. ",
         type =argparse.FileType("w"))
     # Optional arguments.  
     parser.add_argument ("--groupOrderFile",
         help = " Optional file to define the group order, list the groups in a single column in " + \
                 "the order desired. The default ordering is alphabetical.",
         action = "store")
     parser.add_argument ("--useMean",
     help = " Calculate the group values using mean rather than median.",
     action = "store_true")
     parser.add_argument ("--verbose",
     help = " Show runtime messages.",
     action = "store_true")