comparison package_output.py @ 16:4966e095e3c3 draft

planemo upload for repository https://github.com/richard-burhans/galaxytools/tree/main/tools/segalign commit 6cf972d7f1c9ecb097994494a27d00906c6c3e4d

15:99ee8d6f6815

        self,
        pathname: str = "data_package.tgz",
        top_dir: str = "galaxy",
        data_dir: str = "files",
        config_file: str = "commands.json",
    ) -> None:
        self.pathname: str = os.path.realpath(pathname)
        self.data_root: str = os.path.join(top_dir, data_dir)
        self.config_path: str = os.path.join(top_dir, config_file)
        self.config_file: str = config_file
        self.tarfile: typing.Optional[tarfile.TarFile] = None
        self.name_cache: typing.Dict[typing.Any, typing.Any] = {}
        self.working_dir: str = os.path.realpath(os.getcwd())

    def _initialize(self) -> None:

                        sys.exit(f"missing source file {source_path}")

                    self.name_cache[dest_path] = 1
                    # print(f"added: {dest_path}", flush=True)

    def close(self) -> None:
        if self.tarfile is not None:
            self.tarfile.close()
            self.tarfile = None

class bashCommandLineFile:
    def __init__(
        self,
        pathname: str,
        config: configparser.ConfigParser,
        package_file: PackageFile,
    ) -> None:
        self.pathname: str = pathname
        self.config = config
        self.package_file = package_file
        self.executable: typing.Optional[str] = None
        self._parse_lines()

    def _parse_lines(self) -> None:
        with open("commands.json", "w") as ofh:
            with open(self.pathname) as f:
                line: str

            value = rest.pop(0)
            command_dict["args"].append(f"--query={value}")

        return command_dict


class nodevisitor(bashlex.ast.nodevisitor):  # type: ignore[misc]
    def __init__(self, positions: typing.List[typing.Tuple[int, int]]) -> None:
        self.positions = positions
        self.stdin = None

def main() -> None:
    parser = argparse.ArgumentParser()
    parser.add_argument("--tool_directory", type=str, required=True, help="tool directory")
    args = parser.parse_args()

    lastz_command_config_file: str = os.path.join(args.tool_directory, "lastz-cmd.ini")

    config: configparser.ConfigParser = configparser.ConfigParser()
    config.read(lastz_command_config_file)

    package_file = PackageFile()
    lastz_command_file = "lastz-commands.txt"
    bashCommandLineFile(lastz_command_file, config, package_file)
    package_file.close()


if __name__ == "__main__":
    main()

16:4966e095e3c3

        self,
        pathname: str = "data_package.tgz",
        top_dir: str = "galaxy",
        data_dir: str = "files",
        config_file: str = "commands.json",
        format_file: str = "format.txt"
    ) -> None:
        self.pathname: str = os.path.realpath(pathname)
        self.data_root: str = os.path.join(top_dir, data_dir)
        self.config_path: str = os.path.join(top_dir, config_file)
        self.config_file: str = config_file
        self.format_path: str = os.path.join(top_dir, format_file)
        self.format_file: str = format_file
        self.tarfile: typing.Optional[tarfile.TarFile] = None
        self.name_cache: typing.Dict[typing.Any, typing.Any] = {}
        self.working_dir: str = os.path.realpath(os.getcwd())

    def _initialize(self) -> None:

                        sys.exit(f"missing source file {source_path}")

                    self.name_cache[dest_path] = 1
                    # print(f"added: {dest_path}", flush=True)

    def add_format(self, pathname: str) -> None:
        if self.tarfile is None:
            self._initialize()

        source_path = os.path.realpath(pathname)

        if self.tarfile is not None:
            self.tarfile.add(source_path, arcname=self.format_path, recursive=False)

    def close(self) -> None:
        if self.tarfile is not None:
            self.tarfile.close()
            self.tarfile = None

class bashCommandLineFile:
    def __init__(
        self,
        pathname: str,
        config: configparser.ConfigParser,
        args: argparse.Namespace,
        package_file: PackageFile,
    ) -> None:
        self.pathname: str = pathname
        self.config = config
        self.args = args
        self.package_file = package_file
        self.executable: typing.Optional[str] = None
        self._parse_lines()
        self._write_format()

    def _parse_lines(self) -> None:
        with open("commands.json", "w") as ofh:
            with open(self.pathname) as f:
                line: str

            value = rest.pop(0)
            command_dict["args"].append(f"--query={value}")

        return command_dict

    def _write_format(self) -> None:
        if self.args.format_selector == "bam":
            format_name = "bam"
        elif self.args.format_selector == "maf":
            format_name = "maf"
        elif self.args.format_selector == "differences":
            format_name = "interval"
        else:
            format_name = "tabular"

        with open("format.txt", "w") as ofh:
            print(f"{format_name}", file=ofh)

        self.package_file.add_format("format.txt")


class nodevisitor(bashlex.ast.nodevisitor):  # type: ignore[misc]
    def __init__(self, positions: typing.List[typing.Tuple[int, int]]) -> None:
        self.positions = positions
        self.stdin = None

def main() -> None:
    parser = argparse.ArgumentParser()
    parser.add_argument("--tool_directory", type=str, required=True, help="tool directory")
    parser.add_argument("--format_selector", type=str, required=True, help="format selector")
    args = parser.parse_args()

    lastz_command_config_file: str = os.path.join(args.tool_directory, "lastz-cmd.ini")

    config: configparser.ConfigParser = configparser.ConfigParser()
    config.read(lastz_command_config_file)

    package_file = PackageFile()
    lastz_command_file = "lastz-commands.txt"
    bashCommandLineFile(lastz_command_file, config, args, package_file)
    package_file.close()


if __name__ == "__main__":
    main()