display help depending on invocation

#####usage statement#####

SHELL=`readlink -f /proc/$$/exe | cut -d/ -f3`

if [[ $(which launch_universc.sh) != *"not found" ]]

    then

    SHELL='' 

    invocation=$0

else

    SHELL=$(readlink -f /proc/$$/exe | cut -d'/' -f3)

    invocation=$(echo $(basename $0))

fi

help='

Usage:

  '$SHELL' '$(basename $0)' --testrun -t TECHNOLOGY

  '$SHELL' '$(basename $0)' -t TECHNOLOGY --setup

  '$SHELL' '$(basename $0)' -R1 FILE1 -R2 FILE2 -t TECHNOLOGY -i ID -r REFERENCE [--option OPT]

  '$SHELL' '$(basename $0)' -R1 READ1_LANE1 READ1_LANE2 -R2 READ2_LANE1 READ2_LANE2 -t TECHNOLOGY -i ID -r REFERENCE [--option OPT]

  '$SHELL' '$(basename $0)' -f SAMPLE_LANE -t TECHNOLOGY -i ID -r REFERENCE [--option OPT]

  '$SHELL' '$(basename $0)' -f SAMPLE_LANE1 SAMPLE_LANE2 -t TECHNOLOGY -i ID -r REFERENCE [--option OPT]

  '$SHELL' '$(basename $0)' -v

  '$SHELL' '$(basename $0)' -h

  '$SHELL' '$invocation' --testrun -t TECHNOLOGY

  '$SHELL' '$invocation' -t TECHNOLOGY --setup

  '$SHELL' '$invocation' -R1 FILE1 -R2 FILE2 -t TECHNOLOGY -i ID -r REFERENCE [--option OPT]

  '$SHELL' '$invocation' -R1 READ1_LANE1 READ1_LANE2 -R2 READ2_LANE1 READ2_LANE2 -t TECHNOLOGY -i ID -r REFERENCE [--option OPT]

  '$SHELL' '$invocation' -f SAMPLE_LANE -t TECHNOLOGY -i ID -r REFERENCE [--option OPT]

  '$SHELL' '$invocation' -f SAMPLE_LANE1 SAMPLE_LANE2 -t TECHNOLOGY -i ID -r REFERENCE [--option OPT]

  '$SHELL' '$invocation' -v

  '$SHELL' '$invocation' -h

Convert sequencing data (FASTQ) from Nadia or iCELL8 platforms for compatibility with 10x Genomics and run cellranger count