Output calib

define_output now obsolete:
rule define_output
define_ouptut.bsh

Xml

Pixel size variable had wrong variable names

Bug was occuring when sending many batched jobs between resave_hdf5
and registration. The rule registration did not wait until all jobs
of resave_hdf5 were finished. Upon sending registration jobs to the
cluster also some already finished resave_hdf5 jobs were also sent
again. This broke the registration rule since registration jobs were
now sent although some resave_hdf5 jobs were again running and thus
according to snakemake incomplete.
It seems to me that the job files are not deleted fast enough upon
completion. Thus the when registration send its first batch of jobs
out also other finished jobs were resent.
Fixed: registration waits now until all resave_hdf5 jobs are done.
The registration jobs are now send insulated from the resave_hdf5
jobs.

Reinstituted temp files since these were not causing the issue

sending

rule registration is now taking both hdf5_xml and resave_hdf5 ouputs
as input. So the intermediate files of hdf5_xml are not deleted
prematurely.

Fixed channel naming bug in define_output. The channels variable
is overwritten, new variable uses now the correct parameter
for channles

dual channel processing 1 channel contains the beads
reads now the source channel from one parameter in the .yaml file
the settings in the yaml file are now moved up into the common
portion so that they are not overlooked

Naming pattern for tif is now assembled in the .bsh
Channels are taken from central channel setting
Illuminations are taken from central setting but not prepared for
multiple illumination sides!

Update to newest master

Loci - tested and works

Update to latest master

Tools...thanks

Tested single channel tif with LOCI bioformats