Fixed skip and overwrite flags in scripts

Change-Id: Ia43c1ae45f519760c7ef5bf658586be0e39fc038
diff --git a/script/korapxml2krill b/script/korapxml2krill
index 96c3b23..5ec0805 100644
--- a/script/korapxml2krill
+++ b/script/korapxml2krill
@@ -18,6 +18,10 @@
 # 2016/02/04
 # - renamed to korapxml2krill
 # - added Schreibgebrauch support
+#
+# 2016/02/12
+# - fixed foundry skipping
+
 
 sub printhelp {
   print <<'EOHELP';
@@ -27,31 +31,31 @@
 Call:
 korapxml2krill -z --input <directory> --output <filename>
 
---input|-i <directory>          Directory of the document to index
---output|-o <filename>          Document name for output (optional),
-                                Writes to <STDOUT> by default
---overwrite|-w                  Overwrite files that already exist
---token|-t <foundry>[#<layer>]  Define the default tokenization by specifying
-                                the name of the foundry and optionally the name
-                                of the layer. Defaults to OpenNLP#tokens.
---skip|-s <foundry>[#<layer>]   Skip specific foundries by specifying the name
-                                or specific layers by defining the name
-                                with a # in front of the foundry,
-                                e.g. Mate#Morpho. Alternatively you can skip #ALL.
-                                Can be set multiple times.
---allow|-a <foundry>#<layer>    Allow specific foundries and layers by defining them
-                                combining the foundry name with a # and the layer name.
---primary|-p                    Output primary data or not. Defaults to true.
-                                Can be flagged using --no-primary as well.
---human|-m                      Represent the data human friendly,
-                                while the output defaults to JSON
---pretty|-y                     Pretty print json output
---gzip|-z                       Compress the output
-                                (expects a defined output file)
---log|-l                        The Log4perl log level, defaults to ERROR.
---help|-h                       Print this document (optional)
+  --input|-i <directory>          Directory of the document to index
+  --output|-o <filename>          Document name for output (optional),
+                                  Writes to <STDOUT> by default
+  --overwrite|-w                  Overwrite files that already exist
+  --token|-t <foundry>[#<layer>]  Define the default tokenization by specifying
+                                  the name of the foundry and optionally the name
+                                  of the layer. Defaults to OpenNLP#tokens.
+  --skip|-s <foundry>[#<layer>]   Skip specific foundries by specifying the name
+                                  or specific layers by defining the name
+                                  with a # in front of the foundry,
+                                  e.g. Mate#Morpho. Alternatively you can skip #ALL.
+                                  Can be set multiple times.
+  --allow|-a <foundry>#<layer>    Allow specific foundries and layers by defining them
+                                  combining the foundry name with a # and the layer name.
+  --primary|-p                    Output primary data or not. Defaults to true.
+                                  Can be flagged using --no-primary as well.
+  --human|-m                      Represent the data human friendly,
+                                  while the output defaults to JSON
+  --pretty|-y                     Pretty print json output
+  --gzip|-z                       Compress the output
+                                  (expects a defined output file)
+  --log|-l                        The Log4perl log level, defaults to ERROR.
+  --help|-h                       Print this document (optional)
 
-diewald@ids-mannheim.de, 2016/02/04
+diewald@ids-mannheim.de, 2016/02/12
 
 EOHELP
   exit(defined $_[0] ? $_[0] : 0);
@@ -112,8 +116,6 @@
   $main::LAST_STOP = $new;
 };
 
-# Call perl script/korapxml2krill WPD/AAA/00001
-
 # Create and parse new document
 $input =~ s{([^/])$}{$1/};
 my $doc = KorAP::XML::Krill->new( path => $input );
@@ -200,7 +202,8 @@
 else {
   # Add to index file - respect skipping
   foreach my $info (@layers) {
-    unless ($skip{lc($info->[0]) . '#' . lc($info->[1])}) {
+    # Skip if Foundry or Foundry#Layer should be skipped
+    unless ($skip{lc($info->[0])} || $skip{lc($info->[0]) . '#' . lc($info->[1])}) {
       $tokens->add(@$info);
       stop_time;
     };