Add tumor/normal BAM input parameters to command line.

def _add_tumor_params(paired, items, gatk_type):
    """Add tumor/normal BAM input parameters to command line.
    """
    params = []
    if not paired:
        raise ValueError("Specified MuTect2 calling but 'tumor' phenotype not present in batch\n"
                         "https://bcbio-nextgen.readthedocs.org/en/latest/contents/"
                         "pipelines.html#cancer-variant-calling\n"
                         "for samples: %s" % ", " .join([dd.get_sample_name(x) for x in items]))
    if gatk_type == "gatk4":
        params += ["-I", paired.tumor_bam]
        params += ["--tumor-sample", paired.tumor_name]
    else:
        params += ["-I:tumor", paired.tumor_bam]
    if paired.normal_bam is not None:
        if gatk_type == "gatk4":
            params += ["-I", paired.normal_bam]
            params += ["--normal-sample", paired.normal_name]
        else:
            params += ["-I:normal", paired.normal_bam]
    if paired.normal_panel is not None:
        panel_dir = utils.safe_makedir(os.path.join(dd.get_work_dir(items[0]), "mutect2", "panels"))
        normal_panel = vcfutils.bgzip_and_index(paired.normal_panel, items[0]["config"], out_dir=panel_dir)
        if gatk_type == "gatk4":
            params += ["--panel-of-normals", normal_panel]
        else:
            params += ["--normal_panel", normal_panel]
    return params