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
– oguz ismail, Commented Sep 3, 2019 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
– DevanDev, Commented Sep 3, 2019 at 21:18
":TDNUW" - none of the options you specified take any arguments. getopts needs to know which options take argument, which doesn't — KamilCuk
– KamilCuk, Commented Sep 3, 2019 at 21:48
But optarg doesn't now about that. From man optarg : If a character is followed by a <colon>, the option shall be expected to have an argument if it isn't, then it isn't. — KamilCuk
– KamilCuk, Commented Sep 3, 2019 at 21:57

KamilCuk · Accepted Answer · 2019-09-03 22:42:24Z

2

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))

answered Sep 3, 2019 at 22:42

KamilCuk

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