cosmetic: removed mention of no-longer-used options -analysis_topup and -job_topup from the docs

scripts/init_pipeline.pl

 #!/usr/bin/env perl
 
-# A generic loader of hive pipelines.
-#
-# Because all of the functionality is hidden in Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf
-# you can create pipelines by calling the right methods of HiveGeneric_conf directly,
-# so this script is just a commandline wrapper that can conveniently find modules by their filename.
+# A generic script for creating Hive pipelines from PipeConfig module files (see below for docs)
 
 use strict;
 use warnings;
@@ -67,7 +63,7 @@ __DATA__
 
 =head1 SYNOPSIS
 
-    init_pipeline.pl <config_module_or_filename> [-help | [-analysis_topup | -job_topup] <options_for_this_particular_pipeline>]
+    init_pipeline.pl <config_module_or_filename> [<options_for_this_particular_pipeline>]
 
 =head1 DESCRIPTION
 
@@ -81,23 +77,12 @@ __DATA__
         # initialize a generic eHive pipeline:
     init_pipeline.pl Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf -password <yourpassword>
 
-        # see what command line options are available when initializing long multiplication example pipeline
-        #   (assuming your current directory is ensembl-hive/modules/Bio/EnsEMBL/Hive) :
-    init_pipeline.pl PipeConfig/LongMult_conf -help
-
         # initialize the long multiplicaton pipeline by supplying not only mandatory but also optional data:
         #   (assuming your current directory is ensembl-hive/modules/Bio/EnsEMBL/Hive/PipeConfig) :
     init_pipeline.pl LongMult_conf -password <yourpassword> -first_mult 375857335 -second_mult 1111333355556666 
 
 =head1 OPTIONS
 
-    -help            :   Gets this help message and exits
-
-    -analysis_topup  :   A special initialization mode when (1) pipeline_create_commands are switched off and (2) only newly defined analyses are added to the database
-                         This mode is only useful in the process of putting together a new pipeline.
-
-    -job_topup       :   Another special initialization mode when only jobs are created - no other structural changes to the pipeline are acted upon.
-
     -hive_force_init :   If set to 1, forces the (re)creation of the hive database even if a previous version of it is present in the server.
 
 =head1 LICENSE