07f5a53daad64ef67f2ce77de0d5d7076f0548ff
ceisenhart
  Thu May 4 15:34:55 2017 -0700
Fixing an error in documentation spotted by Chris Lee, refs 18736

diff --git src/utils/expMatrixToBarchartBed/expMatrixToBarchartBed src/utils/expMatrixToBarchartBed/expMatrixToBarchartBed
index f74e1d7..d3b4bd8 100755
--- src/utils/expMatrixToBarchartBed/expMatrixToBarchartBed
+++ src/utils/expMatrixToBarchartBed/expMatrixToBarchartBed
@@ -6,38 +6,37 @@
 import os
 import sys
 import argparse
 import tempfile
 
 def parseArgs(args):
     """
     Parse the command line arguments.
     """
     parser= argparse.ArgumentParser(description = __doc__)
     parser.add_argument ("metaFile",
         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 first row should start with a hashtag, e.g. #." + \
-                "the samples in the first row should exactly match the ones in " + \
+            help = " The input matrix file. The samples in the first row should exactly match the ones in " + \
                 "the metaFile. The labels (ex ENST*****) in the first column should exactly match " + \
                 "the ones in the coordinate file.",
         type = argparse.FileType("r"))
     parser.add_argument ("coordinateMap",
-        help = " Six column no header,  maps the column labels from the matrix to coordinates. Tab " + \
-                "separated; label, chr, strand, start coord, end coord, gene name. ",
+        help = " Bed5+1 format. File that maps the column labels from the matrix to coordinates. Tab " + \
+                "separated; chr, start coord, end coord, label, strand, gene name. ",
         action = "store")
     parser.add_argument ("outputFile",
         help = " The output file. ",
         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")