picard improvements (sort order)

[bernt-matthias]

• picard MarkDup*: remove ASSUME_SORTED because deprepated (for ASSUME_SORT_ORDER) and the info is in the metadata
• remove ASSUME_SORTED and use metadata

In both cases we might also think about to omit ASSUME_SORTED="false" or ASSUME_SORT_ORDER="unsorted", resp., because then picard should just use the info in the header.

• Remove some test parameters that are not (yet) implemented by the tool Fix test parameters that are not defined in the inputs #4095
• MarkDuplicates: remove max from OPTICAL_DUPLICATE_PIXEL_DISTANCE; fixes Picard MarkDuplicates: OPTICAL_DUPLICATE_PIXEL_DISTANCE  #4500
• allow unsorted.bam (ie all bam types) as input for most of the touched tools (except for the mark duplicates tools which seem to need coord or qname sorted bam) .. I guess there are more which could take unsorted.bam
• allow unsorted.bam also for most of the other types (in particular if sam was supported)

TODO:

• remane Collect Alignment Summary Metrics writes a file containing summary alignment metrics to the name of the underlying tool

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