comparison qualimap_bamqc.py @ 42:c53375e61b33 draft

planemo upload for repository https://github.com/scottx611x/qualimap2 commit 9fafbbc012490e70d06fcef4704a1e4a45b382c5-dirty

41:e856fda6f375

from subprocess import check_call, CalledProcessError
import shutil
import sys


def qualimap_bamqc(bam_filename, genomecov_file, out_dir, jv_mem_size):
    qualimap_command = [
        "qualimap", "bamqc",
        "-bam " + bam_filename,
        "-oc " + genomecov_file,
        "-outdir " + out_dir,
        "--java-mem-size=" + jv_mem_size
    ]

    try:

def main():
    parser = argparse.ArgumentParser(
        description="Generate Bam Quality Statistics"
    )
    parser.add_argument('--input_file')
    parser.add_argument('--out_genome_file')
    parser.add_argument('--out_dir')
    parser.add_argument('--out_zip')
    parser.add_argument('--out_html')
    parser.add_argument('--out_results')
    parser.add_argument('--java_mem_size')

    args = parser.parse_args()
    print(args)

    qualimap_bamqc(
        args.input_file,
        args.out_genome_file,
        args.out_dir,
        args.java_mem_size
    )

    shutil.make_archive(
        'raw_data_qualimapReport',
        'zip',
        os.path.join(args.out_dir,'raw_data_qualimapReport')
    )

    shutil.move("raw_data_qualimapReport.zip", args.out_zip)
    shutil.move(
        os.path.join(args.out_dir, "genome_results.txt"),
        args.out_results
    )
    shutil.move(
        os.path.join(args.out_dir, "qualimapReport.html"),
        args.out_html
    )

if __name__ == "__main__":
    main()

42:c53375e61b33

from subprocess import check_call, CalledProcessError
import shutil
import sys


def qualimap_bamqc(bam_filename, out_dir, jv_mem_size):
    qualimap_command = [
        "qualimap", "bamqc",
        "-bam " + bam_filename,
        "-outdir " + out_dir,
        "--java-mem-size=" + jv_mem_size
    ]

    try:

def main():
    parser = argparse.ArgumentParser(
        description="Generate Bam Quality Statistics"
    )
    parser.add_argument('--input_file')
    parser.add_argument('--out_dir')
    parser.add_argument('--out_zip')
    parser.add_argument('--out_html')
    parser.add_argument('--java_mem_size')

    args = parser.parse_args()
    print(args)

    qualimap_bamqc(
        args.input_file,
        args.out_dir,
        args.java_mem_size
    )

    shutil.make_archive(
        'raw_data_qualimapReport',
        'zip',
        os.path.join(args.out_dir, 'raw_data_qualimapReport')
    )

    shutil.move("raw_data_qualimapReport.zip", args.out_zip)
    shutil.move(
        os.path.join(args.out_dir, "genome_results.txt"),
        args.out_results
    )

if __name__ == "__main__":
    main()