comparison data_manager/data_manager_humann2_download.py @ 5:ff9cf22838d4 draft default tip

"planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/data_managers/data_manager_humann2_database_downloader commit 02d2967f77e3fa5a18aea63dc84aa9ab418dc165"

4:9244804f69a7

    NB the directory pointed to by 'extra_files_path'
    doesn't exist initially, it is the job of the script
    to create it if necessary.

    """
    params = json.loads(open(jsonfile).read())
    return (params['param_dict'],
            params['output_data'][0]['extra_files_path'])


# Utility functions for creating data table dictionaries

# Example usage:
# >>> d = create_data_tables_dict()
# >>> add_data_table(d,'my_data')
# >>> add_data_table_entry(dict(dbkey='hg19',value='human'))
# >>> add_data_table_entry(dict(dbkey='mm9',value='mouse'))
# >>> print str(json.dumps(d))
def create_data_tables_dict():
    """Return a dictionary for storing data table information

    Returns a dictionary that can be used with 'add_data_table'
    and 'add_data_table_entry' to store information about a

      database: database to download (chocophlan or uniref)
      build: build of the database to download
      target_dir: directory to put copy or link to the data file

    """
    value = "%s-%s-%s" % (database, build, datetime.date.today().isoformat())
    db_target_dir = os.path.join(target_dir, database)
    build_target_dir = os.path.join(db_target_dir, build)
    cmd = "humann2_databases --download %s %s %s --update-config no" % (
        database,
        build,
        db_target_dir)
    subprocess.check_call(cmd, shell=True)
    shutil.move(os.path.join(db_target_dir, database), build_target_dir)

        options.build,
        target_dir)

    # Write output JSON
    print("Outputting JSON")
    print(str(json.dumps(data_tables)))
    open(jsonfile, 'wb').write(json.dumps(data_tables))
    print("Done.")

5:ff9cf22838d4

    NB the directory pointed to by 'extra_files_path'
    doesn't exist initially, it is the job of the script
    to create it if necessary.

    """
    with open(jsonfile) as fh:
        params = json.load(fh)
    return (params['param_dict'],
            params['output_data'][0]['extra_files_path'])


# Utility functions for creating data table dictionaries

# Example usage:
# >>> d = create_data_tables_dict()
# >>> add_data_table(d,'my_data')
# >>> add_data_table_entry(dict(dbkey='hg19',value='human'))
# >>> add_data_table_entry(dict(dbkey='mm9',value='mouse'))
# >>> print(json.dumps(d))
def create_data_tables_dict():
    """Return a dictionary for storing data table information

    Returns a dictionary that can be used with 'add_data_table'
    and 'add_data_table_entry' to store information about a

      database: database to download (chocophlan or uniref)
      build: build of the database to download
      target_dir: directory to put copy or link to the data file

    """
    value = "{}-{}-{}".format(database, build, datetime.date.today().isoformat())
    db_target_dir = os.path.join(target_dir, database)
    build_target_dir = os.path.join(db_target_dir, build)
    cmd = "humann2_databases --download {} {} {} --update-config no".format(
        database,
        build,
        db_target_dir)
    subprocess.check_call(cmd, shell=True)
    shutil.move(os.path.join(db_target_dir, database), build_target_dir)

        options.build,
        target_dir)

    # Write output JSON
    print("Outputting JSON")
    with open(jsonfile, 'w') as fh:
        json.dump(data_tables, fh, sort_keys=True)
    print("Done.")