rule tool-a:
        input:
            counts=config['general']['paths']["count_matrix"]

        output:
            os.path.join(config['general']['paths']['outdir'], 'diff','tool-a', 'tool-a.tsv')
        params:
            result_dir=os.path.join(config['general']['paths']['outdir'], 'diff','tool-a')

        shell:
            """
            mkdir -p {params.result_dir}
            Rscript {GENE_TEST_DIFF_SCRIPT} {input.counts} {params.result_dir}
            """

rule tool-b:
    input:
        counts=config['general']['paths']["count_matrix"]

    output:
        os.path.join(config['general']['paths']['outdir'], 'diff','tool-b', 'tool-b.tsv')

    params:
        result_dir=os.path.join(config['general']['paths']['outdir'], 'diff','tool-b')
    shell:
        """
        mkdir -p {params.result_dir}
        Rscript {GENE_TEST_DIFF_SCRIPT} {input.counts}
        """

import pandas as pd
from snakemake.utils import min_version
import itertools

### set min snakemake requirement
min_version("5.4.1")

### load config
configfile: "config.yaml"

### load sample data

DIFF_METH  = config['general']['method']
Tool_a  = config['general']['paths']['tool_a-script']
Tool_b      = config['general']['paths']['tool_b-script']

if DIFF_METH == "tool-a":
    GENE_TEST_DIFF_SCRIPT   = Tool_a
elif DIFF_METH == "tool-b":
    GENE_TEST_DIFF_SCRIPT   = Tool_b
else:
    sys.exit("Invalid value for 'method', possible choices are: 'tool-a' and 'tool-b'")

onstart:
    sys.stderr.write("GENE_DIFF_METH = " + GENE_DIFF_METH + "n")
    return []

### define rules not to be executed on the cluster
localrules: all

### define target rules
rule all:
    input:
        expand(os.path.join(config['general']['paths']['outdir'], 'diff','tool-a','tool-a.tsv')),
        expand(os.path.join(config['general']['paths']['outdir'], 'diff','tool-b','tool-b.tsv')),



include: "rules/tools.smk"

general:
    gene_diff_method: 'tool-b'