comparison qualimap_bamqc.py @ 32:90170eb47bd1 draft

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

31:a77bae54b1c7

#!/usr/bin/env python
from __future__ import print_function
import argparse
from subprocess import check_call, CalledProcessError
import shutil
import sys

OUTPUT_DIR = "qualimap_results"

    parser.add_argument('--out_genome_file')
    parser.add_argument('--java_mem_size')

    args = parser.parse_args()

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

32:90170eb47bd1

#!/usr/bin/env python
from __future__ import print_function
import argparse
import os
from subprocess import check_call, CalledProcessError
import shutil
import sys

OUTPUT_DIR = "qualimap_results"

    parser.add_argument('--out_genome_file')
    parser.add_argument('--java_mem_size')

    args = parser.parse_args()

    print(os.listdir(OUTPUT_DIR))

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