The commands are shell commands (terminal of your linux computer).

Did you read the manual?

For example the adapter is "TGGAATTCTCGGGTGCCAAGG"

So you will use it from terminal like this:

cutadapt -a TGGAATTCTCGGGTGCCAAGG good_reads.fastq > trimed_good_reads.fastq

If you wanna use it in python script it will be like that

def run_cutadapt(adaptor, input_file, output_file):
    cutadapt = subprocess.Popen(["cutadapt", "-a", adaptor, input_file, "-o",                  output_file], stdout=subprocess.PIPE)
    output = cutadapt.communicate()[0]

    return output