comparison qualimap_bamqc.py @ 41:e856fda6f375 draft

planemo upload for repository https://github.com/scottx611x/qualimap2 commit dc78b7c4b1780b316ca4aba2be247969ac1100ec-dirty

40:98944e914637

        description="Generate Bam Quality Statistics"
    )
    parser.add_argument('--input_file')
    parser.add_argument('--out_genome_file')
    parser.add_argument('--out_dir')
    parser.add_argument('--java_mem_size')

    args = parser.parse_args()
    print(args)

    output_dir = os.path.dirname(args.out_genome_file)

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

    )

    shutil.make_archive(
        'raw_data_qualimapReport',
        'zip',
        args.out_dir + '/raw_data_qualimapReport'
    )

    shutil.move(
        "raw_data_qualimapReport.zip",
        os.path.join(output_dir, "raw_data_qualimapReport.zip")
    )

    [
        shutil.move(
            os.path.join(args.out_dir, file_name),
            os.path.join(output_dir, file_name)
        )
        for file_name in ["genome_results.txt", "qualimapReport.html"]
    ]

if __name__ == "__main__":
    main()

41:e856fda6f375

        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,

    )

    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()