comparison data_manager/ariba_database_builder.py @ 9:218301fbbb99 draft default tip

"planemo upload for repository https://github.com/thanhleviet/galaxy-tools commit 3a0b92d1a2dcd5c5b75e5b63727850139af21ace-dirty"

8:fb4da292b6d0

import argparse
import json
import os
import shutil
import errno


data_table_name = "ariba_databases"

mlst_dict = {
    "achs"	: "Achromobacter spp.",

}


genes_dict = {
    "card" : "CARD",
    "resfinder" : "Resfinder",
    "plasmidfinder" : "Plasmidfinder",
    "megares" : "Megares",
    "argannot" : "Argannot",
    "vfdb_core" : "vfdb_core",

    elif args.database_type == "fasta":
        build_custom_db(args.fasta, args.coding, args.db_name)
        name = args.db_name

    params = json.loads(open(args.params).read())
        
    target_directory = params['output_data'][0]['extra_files_path']
    
    if not os.path.isdir(target_directory):
      os.mkdir(target_directory)

9:218301fbbb99

import argparse
import json
import os
import shutil
import errno
from pprint import pprint

data_table_name = "ariba_databases"

mlst_dict = {
    "achs"	: "Achromobacter spp.",

}


genes_dict = {
    "card" : "CARD",
    "ncbi" : "ncbi",
    "resfinder" : "Resfinder",
    "plasmidfinder" : "Plasmidfinder",
    "megares" : "Megares",
    "argannot" : "Argannot",
    "vfdb_core" : "vfdb_core",

    elif args.database_type == "fasta":
        build_custom_db(args.fasta, args.coding, args.db_name)
        name = args.db_name

    params = json.loads(open(args.params).read())
    pprint(params)    
    target_directory = params['output_data'][0]['extra_files_path']
    
    if not os.path.isdir(target_directory):
      os.mkdir(target_directory)