Picard FixMateInformation does not launch individual jobs when multiple datasets are selected

[jennaj]

Tool version: https://toolshed.g2.bx.psu.edu/view/devteam/picard/00fe2ff64467

Problem: Tool attempts to execute using all selected inputs in one job, then fails. If run on one dataset at a time (same datasets that fail with multi-select), the jobs are successful.

Error example:

Dataset generation errors
Dataset 71: FixMateInformation on data 31 and data 27: BAM with fixed mates
Tool execution generated the following error message:
Fatal error: Exit code 1 ()
Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/galaxy-repl/main/scratch -Xmx7680m -Xms256m
Exception in thread "main" htsjdk.samtools.SAMException: Cannot read non-existent file: /galaxy-repl/main/files/XXX/XXX/dataset_XXX.dat,/galaxy-repl/main/files/XXX/XX/dataset_XXX.dat
at htsjdk.samtools.util.IOUtil.assertFileIsReadable(IOUtil.java:308)
at picard.sam.FixMateInformation.doWork(FixMateInformation.java:107)
at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:206)
at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:95)
at picard.cmdline.PicardCommandLine.main(PicardCommandLine.java:105)

cc @galaxyproject/guac