fixed the cbm converter
uncommented one test
resolve eclipse warnings
Added --header --footer --submit parameters
Removed redundant skip statement from header
Functions getFile, putFile, alloutputsexist and so are now part of the header (pbs, local)
In submit.ftl.sh scripts: # First cd to the directory with the *.sh and *.finished scripts
Merge branch 'master' of github.com:molgenis/molgenis
Merge pull request #519 from RoanKanninga/master

Fixed CBM converter
Merge branch 'master' of https://github.com/molgenis/molgenis
Merge pull request #526 from mdijkstra/master

see commit msg's
Merge branch 'master' of https://github.com/molgenis/molgenis
Updated manual
added clear functionality
Merge pull request #521 from georgebyelas/master

uncommented one test, that is working
added some tests
Merge pull request #530 from georgebyelas/master

small add to tests
made default queue - none; issue #524
added filtering of parameters, that start with cypher; issue #527
Merge pull request #531 from georgebyelas/master

filter parameters, that start with cypher + tests