add --trackLabel to bam-to-json.pl, and make it a required arg

Arabidopsis-Information-Portal · Feb 15, 2012 · f28d576 · f28d576
1 parent 68d5913
commit f28d576
Show file tree

Hide file tree

Showing 2 changed files with 8 additions and 3 deletions.
diff --git a/bin/bam-to-json.pl b/bin/bam-to-json.pl
@@ -9,7 +9,7 @@ =head1 USAGE
   bam-to-json.pl                               \
       --bam <bam file>                         \
       [ --out <output directory> ]             \
-      [ --tracklabel <track identifier> ]      \
+      [ --trackLabel <track identifier> ]      \
       [ --key <human-readable track name> ]    \
       [ --cssClass <class> ]                   \
       [ --clientConfig '{ JSON }' ]            \
@@ -28,6 +28,10 @@ =head1 OPTIONS
 
 Required.  BAM file to read and format.
 
+=item --trackLabel <track identifier>
+
+Unique identifier for this track.  Required.
+
 =item --out <directory>
 
 Output directory to write to.  Defaults to C<data/>.
@@ -77,7 +81,7 @@ =head1 OPTIONS
 my $outdir = "data";
 my $help;
 GetOptions("out=s" => \$outdir,
-	   "tracklabel=s" => \$trackLabel,
+	   "tracklabel|trackLabel=s" => \$trackLabel,
 	   "key=s" => \$key,
            "bam=s" => \$bamFile,
            "cssClass=s", \$cssClass,
@@ -89,6 +93,7 @@ =head1 OPTIONS
 
 pod2usage( -verbose => 2 ) if $help;
 pod2usage( 'Must pass a --bam argument.' ) unless defined $bamFile;
+pod2usage( 'Must pass a --trackLabel argument.' ) unless defined $trackLabel;
 
 if (!defined($nclChunk)) {
     # default chunk size is 50KiB

diff --git a/bin/flatfile-to-json.pl b/bin/flatfile-to-json.pl
@@ -44,7 +44,7 @@ =head2 REQUIRED
 
 =item --trackLabel <track identifier>
 
-Unique identifier for this track.
+Unique identifier for this track.  Required.
 
 =back
-Original file line number
+Diff line change
@@ Expand Up / @@ -44,7 +44,7 @@ =head2 REQUIRED @@
     =item --trackLabel <track identifier>
-    Unique identifier for this track.
+    Unique identifier for this track.  Required.
     =back
@@ Expand Down @@