@follows(mkdir("metaphlan.dir"))
@transform( SEQUENCEFILES,
            SEQUENCEFILES_REGEX
            , r"metaphlan.dir/\1.relab")
def buildMetaphlanRelativeAbundance(infile, outfile):
    to_cluster = True
    # at present the pipeline will take a set of files
    # and compute the abundances of different taxonomic groups
    # based on ALL reads i.e. paired data are combined into
    # a single file for analysis
    if PARAMS["metaphlan_executable"] == "bowtie2":
        assert os.path.exists(PARAMS["metaphlan_db"] + ".1.bt2"), "missing file %s: Are you sure you have the correct database for bowtie2?" % PARAMS["metaphlan_db"] + ".1.bt2"
        method = "--bowtie2db"
    elif PARAMS["metaphlan_executable"] == "blast":
        assert os.path.exists(PARAMS["metaphlan_db"] + "nin"), "missing file %s: Are you sure you have the correct database for bowtie2?" % PARAMS["metaphlan_db"] + "nin"
        method = "--blastdb"

    statement = PipelineGenomeAssembly.Metaphlan().build(infile, method="rel_ab")
    P.run()

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update_locator updates the application state to ensure that any
dataset/ETHPy150Open CGATOxford/cgat/obsolete/pipeline_genomeassembly.py/buildMetaphlanRelativeAbundance--crossover with--dataset/ETHPy150Open VisTrails/VisTrails/vistrails/core/application.py/VistrailsApplicationInterface.update_locator