update & refactor test cases

[stevekm]

the following test cases need to be updated to use the PlutoTestCase class so that they can be controlled with the now-standard pluto interfaces

$ find tests/ -name "*.py" -exec grep -l "unittest.TestCase" {} \;
tests/test_facets-workflow_cwl.py
tests/test_run-facets-legacy-wrapper_cwl.py
tests/test_snp-pileup-wrapper_cwl.py
tests/test_paste-col_cwl.py
tests/test_maf_col_filter_cwl.py
tests/test_add_is_in_impact.py
tests/test_update_cBioPortal_data.cwl.py
tests/test_put_in_dir.py
tests/test_replace_cwl.py
tests/test_run-facets-wrapper_cwl.py
tests/test_reduce_sig_figs.py
tests/test_analysis-workflow_cwl.py
tests/test_copy_number.py
tests/test_fusion_filter_cwl.py
tests/test_maf_filter_cwl.py
tests/test_concat_with_comments_cwl.py

[stevekm]

this is completed in dev