Update to use revised pbcore PBToolRunner

[Tracking bug 22690]

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/pbh5tools/": change = 122549]
Forgot to fix these guys

[Tracking bug 22690]

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/pbh5tools/": change = 122557]