import argparse
import glob, os
import trackhub
import random

parser = argparse.ArgumentParser()
parser.add_argument("--hub_name", help="Required. the name of your track hub")
parser.add_argument("--genome", help="Required. the version of genome")
parser.add_argument("--sample_name",nargs='+', help="Required. name of your samples")
parser.add_argument("--bw", nargs='+', help = "BigWig files to be added to the hub")
parser.add_argument("--peaks", nargs = '+', help = "Called peaks in bed format")
parser.add_argument("--diff_peaks", nargs = '+', help = "Called differential peaks in bigBed format")
parser.add_argument("--categories", nargs='+', help= "TF or Histone marks. If provided, file names will be searched for pattern provided by this option. Then tracks will be aggregated based on those categories")
parser.add_argument("--category_colors", nargs = '+', help = "Specified colors for each categories")
parser.add_argument("--output_dir", help="the folder where the hub track files are generated, default is the same as input_dir", default=".")
parser.add_argument("--email", help="Required. your email to contact")
parser.add_argument("--composite_track_name", help="Required. the name of your composite track")

args = parser.parse_args()

print(args.hub_name)
print(args.genome)
print(args.sample_name)
print(args.bw)
print(args.peaks)
print(args.categories)
print(args.category_colors)
print(args.output_dir)
print(args.email)
print(args.diff_peaks)