add GATK2 wrapper, initial work was done by the Galaxy Core Team and James Johnson
add an whitespace to prevent to TS to replace the entire tag
Various corrections.
Remove double quotes.

Fix:
- ERROR MESSAGE: Invalid value "NO_ET" specified for argument phone_home; valid options are (NO_ET,AWS,STDOUT).
- ERROR MESSAGE: Couldn't read file ...
Sample files should not contain uncommented lines.
HaplotypeCaller support multiple BAM files.
adopt to recent changes in GATK 2.7
Merge branch 'master' of https://github.com/bgruening/galaxytools
Fix typo.
Standardise --dbsnp option using macros when possible.

Bugfix: in unified_genotyper.xml it was possible to specify the option more
than once, which causes a GATK error.
Fix for "(ERROR/3) At least one body element must separate transitions; adjacent transitions are not allowed."
Fix tools which do not support parallel execution with --num_threads .
Remove undocumented development-only parameter.

See http://gatkforums.broadinstitute.org/discussion/2115/what-do-the-different-parameters-for-the-unifiedgenotyper-p-nonref-model-mean
Add an (unsatisfied) gatk2 package requirement.

This is useful for system administrators which need to load modules
(e.g. JDK 1.7) by adding appropriate commands to
<tool_dependencies_dir>/gatk2/default/env.sh .
removing threads and num_cpu_threads_per_data_thread from tools that did not support it
merge
Add documentation for commit a06a5b32ba5f1a34360055770f8488fb24b4d96b .
seems that --num_cpu_threads_per_data_tread is working for Nicola, reenable it
Merge branch 'master' of https://github.com/bgruening/galaxytools
Fix double help in some params by merging.