def bowtie(sam, btd, f, r, u, opt, no_shrink, threads):
bt2 = '<STR_LIT>' % (btd, threads)<EOL>if f is not False:<EOL><INDENT>bt2 += '<STR_LIT>' % (f, r)<EOL><DEDENT>if u is not False:<EOL><INDENT>bt2 += '<STR_LIT>' % (u)<EOL><DEDENT>bt2 += opt<EOL>if no_shrink is False:<EOL><INDENT>if f is False:<EOL><INDENT>bt2 += '<STR_LIT>' % (sam)<EOL><DEDENT>else:<EOL><INDENT>bt2 += '<STR_LIT>' % (sam)<EOL><DEDENT><DEDENT>else:<EOL><INDENT>bt2 += '<STR_LIT>' % (sam)<EOL><DEDENT>return bt2<EOL>
generate bowtie2 command