annotate data_manager/rna_star_index_builder.py @ 5:f5eb9afa8f8a draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 9b68f6ae375aed38493f8399b8572347c750336d

#!/usr/bin/env python

import argparse
import json


def main():
    parser = argparse.ArgumentParser()
    parser.add_argument( '--config-file' )
    parser.add_argument( '--value' )
    parser.add_argument( '--dbkey' )
    parser.add_argument( '--name' )
    parser.add_argument( '--subdir' )
    parser.add_argument( '--data-table' )
    parser.add_argument( '--with-gene-model', action='store_true' )
    parser.add_argument( '--index-version' )

    args = parser.parse_args()

    if args.dbkey in [ None, '', '?' ]:
        raise Exception( '"%s" is not a valid dbkey. You must specify a valid dbkey.' % ( args.dbkey ) )

    with_gene_model = "0"
    if args.with_gene_model:
        with_gene_model = "1"

    data_manager_dict = {'data_tables': {args.data_table: [dict({"value": args.value, "dbkey": args.dbkey, "name": args.name, "path": args.subdir, "with_gene_model": with_gene_model, "version": args.index_version} )]}}
    open( args.config_file, 'w' ).write( json.dumps( data_manager_dict ) )


if __name__ == "__main__":
    main()