GNU Astronomy Utilities manual

4.1.1 Arguments and options

On the command line, the first thing you enter is the name of the program you want to run. After that you can specify two types of input: arguments and options. Arguments are those tokens that are not preceded by any hyphens (-), the program is suppose to understand what they are without any help from the user.

Arguments can be both mandatory and optional and since there is no help from you, their order might also matter (for example in cp which is used for copying). The outputs of --usage and --help shows which arguments are optional and which are mandatory, see --usage. As their name suggests, options are only optional and most of the time you don’t have to worry about what order you specify them in.

In case your arguments or option values contain any of the shell’s meta-characters, you have to quote them. If there is only one such character, you can use a backslash (\) before it. If there are multiple, it might be easier to simply put your whole argument or option value inside of double quotes ("). In such cases, everything inside the double quotes will be seen as one ‘word’.

For example let’s say you want to specify the Header data unit (HDU) of your FITS file using a complex expression like 3; images(exposure > 100). If you simply add these after the --hdu (-h) option, the programs in Gnuastro will read the value to the HDU option as 3 and run. Then, Bash will attempt to run a separate command images(exposure > 100) and complain about a syntax error. This is because the semicolon (;) is an ‘end of command’ character in Bash. To solve this problem you can simply put double quotes around the whole string you want to pass as seen below:

$ astimgcrop --hdu="3; images(exposure > 100)" FITSimage.fits

Alternatively you can put a \ before every metacharacter in this string, but probably you will agree with us that the double quotes are much more easier, elegant and readable.

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GNU Astronomy Utilities manual, November 2015.