The decompiler supports the batch mode operation with the text and GUI versions of IDA Pro. All you need is to specify the -Ohexrays switch in the command line. The format of this switch is:
The valid options are:
The output file name can be prepended with + to append to it. If the specified file extension is invalid, .c will be used.
The functions can be specified by their addresses or names. The ALL keyword means all non-library functions. For example:
will decompile all nonlibrary functions to outfile.c. In the case of an error, the .idb file will be sent to hex-rays.com. The -A switch is necessary so avoid the initial dialog boxes.