Problem in passing command line arguments using getopts

Question

I am trying to pass commandline arguments to my workflow script using getopts but the code throws an error

Following is the snippet of code for passing command line arguments

# take strings as arguments.
while getopts "TDNUW:" opt; do
  case "$opt" in
     T) T="$OPTARG" ;;
     D) D="$OPTARG" ;;
     N) N="$OPTARG" ;;
     U) U="$OPTARG" ;;
     W) W="$OPTARG" ;;
     \?) echo "Usage:[-T T1wfilename] [-D Dfilename] [-N Stream_Number] [-U User] [-W Workflow]";;

    esac
  done 
 shift $(expr $OPTIND - 1)

#Subjects Directory with $U : UserId

SUBJECTS_DIR=/Bio/Bmax/data/imaging_data/$U

#Subjects path with $W : workflow number    

SUBJECT_PATH=$SUBJECTS_DIR/$W

I have tried calling the script using the options

./code.sh -T dummy_t1t2.nii.gz -D dummy_dti.nii.gz -N 100000 -U Markus -W Workflow_000000000000334

and i am encountering an error

Error: input image /Bio/Bmax/data/imaging_data/// not valid

The arguments that i have passed through commandline are not interpreted by the code, could some one please provide me some hint why my script could not recognize the arguments.

You're not assigning anything to variables U and W, what were you expecting? — oguz ismail, Sep 03 '19 at 18:48
I am assigning -U Markus -W Workflow_000000000000334 two values to parameters -U and -W, is it a wrong way to assign the variables ? — DevanDev, Sep 03 '19 at 21:18
You assign `argument="$OPTARG"` and `String="$OPTARG"`. You assign variables named `argument` and `String`, not `U` or `W`. — KamilCuk, Sep 03 '19 at 21:24
@KamilCuk Yes, now i have altered my script,but still the file dummy_t1t2.nii.gz that i have passed to the variable -T is not recognized — DevanDev, Sep 03 '19 at 21:37
`":TDNUW"` - none of the options you specified take any arguments. `getopts` needs to know which options take argument, which doesn't — KamilCuk, Sep 03 '19 at 21:48
@KamilCuk , all options take arguments and the arguments are provided through command line — DevanDev, Sep 03 '19 at 21:55
But `optarg` doesn't now about that. From [man optarg](http://man7.org/linux/man-pages/man1/getopts.1p.html) : `If a character is followed by a , the option shall be expected to have an argument` if it isn't, then it isn't. — KamilCuk, Sep 03 '19 at 21:57

score 2 · Accepted Answer · answered Sep 03 '19 at 22:42

You need to assign the variables you want to use manually. getopts doesn't do the work for you.

You need a : after each letter option to tell getopts it is a option that takes argument.

while getopts "T:D:N:U:W:" opt; do
  case "$opt" in
     T) T="$OPTARG" ;;
     D) D="$OPTARG" ;;
     N) N="$OPTARG" ;;
     U) U="$OPTARG" ;;
     W) W="$OPTARG" ;;
     \?) echo "Usage:[-T T1wfilename] [-D Dfilename] [-N Stream_Number] [-U User] [-W Workflow]" ;;
    esac
 done 
 shift $((OPTIND - 1))

Problem in passing command line arguments using getopts

1 Answers1