--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/changeCase.pl	Tue Dec 04 10:49:46 2012 -0500
@@ -0,0 +1,58 @@
+#! /usr/bin/perl -w
+
+use strict;
+use warnings;
+
+my $columns = {};
+my $del = "";
+my @in = ();
+my @out = ();
+my $command = "";
+my $field = 0;
+
+# a wrapper for changing the case of columns from within galaxy
+# isaChangeCase.pl [filename] [columns] [delim] [casing] [output]
+
+die "Check arguments: $0 [filename] [columns] [delim] [casing] [output]\n" unless @ARGV == 5;
+
+# process column input
+$ARGV[1] =~ s/\s+//g;
+foreach ( split /,/, $ARGV[1] ) {
+  if (m/^c\d{1,}$/i) {
+    s/c//ig;
+    $columns->{$_} = --$_;
+  }
+}
+
+die "No columns specified, columns are not preceeded with 'c', or commas are not used to separate column numbers: $ARGV[1]\n" if keys %$columns == 0;
+
+my $column_delimiters_href = {
+	'TAB' => q{\t},
+	'COMMA' => ",",
+	'DASH' => "-",
+	'UNDERSCORE' => "_",
+	'PIPE' => q{\|},
+	'DOT' => q{\.},
+	'SPACE' => q{\s+}
+};
+	
+$del = $column_delimiters_href->{$ARGV[2]};
+
+open (OUT, ">$ARGV[4]") or die "Cannot create $ARGV[4]:$!\n";
+open (IN,  "<$ARGV[0]") or die "Cannot open $ARGV[0]:$!\n";
+while (<IN>) {
+  chop;
+  @in = split /$del/; 
+  for ( my $i = 0; $i <= $#in; ++$i) {
+	if (exists $columns->{$i}) {
+		push(@out, $ARGV[3] eq 'up' ? uc($in[$i]) : lc($in[$i]));
+	} else {
+		push(@out, $in[$i]);
+	}
+  }
+  print OUT join("\t",@out), "\n";
+  @out = ();
+}
+close IN;
+
+close OUT;