The decompiler supports the batch mode operation with the text and GUI versions of IDA. 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 to decompile 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 to avoid the initial dialog boxes.