view create_config_file.py @ 0:dd513c72ea56 draft

planemo upload for repository https://github.com/portiahollyoak/Tools commit 1f1c277219ca756c9baa453592b455597fd593d8-dirty

import argparse


description = ("This script will create a configuration file for samples to be run in Pindel")


parser = argparse.ArgumentParser()
parser.add_argument("--input_file", nargs="*", help="One or more alignment files")
parser.add_argument("--insert_size", nargs="+", help="Expected Insert size")
parser.add_argument("--sample_label", nargs="+", help="Sample label")
parser.add_argument("--output_config_file", help="Output config file")
args = parser.parse_args()

template = "{input_file}\t{insert_size}\t{sample_label}\n"
with open(args.output_config_file, "w") as output:
    for input_file, insert_size, sample_label in zip(args.input_file, args.insert_size, args.sample_label):
        config_line = template.format(input_file=input_file, insert_size=insert_size, sample_label=sample_label)
        output.write(config_line)