Commit 47b369f6 authored by TomKellyGenetics's avatar TomKellyGenetics
Browse files

correct passing arguments

parent d75ef5ed
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+17 −7
Original line number Diff line number Diff line
@@ -61,10 +61,22 @@ supported software be used for other purposes.

The code in this repository is licensed under the MIT License.
'
##########




#####print usage#####
if [[ -z $1 ]]; then
    echo "$statement"
    exit 1
fi
##########

#variable optionsname=false



#####declare variables#####
name=$1
type=$2
inpath=""
@@ -95,7 +107,9 @@ if [[ $1 == "-v" ]] || [[ $2 == "-v" ]] || [[ $1 == "--version" ]] || [[ $2 == "
    end=true
    version=true
fi
for op in "${@:3}"; do
shift
shift
for op in "${@}"; do
    if $next; then
        next=false;
        continue;
@@ -109,6 +123,7 @@ for op in "${@:3}"; do
                shift
            else
                echo "Explicit setting of input using other flags will override inputs found with --inpath"
                shift
            fi
            ;;
           --output)
@@ -270,11 +285,6 @@ for op in "${@:3}"; do
done
##########

if [[ -z $1 ]]; then
    echo "$statement"
    exit 1
fi

if [[ $end  ]]; then
    if [[ ! -z $help ]]; then
        echo "$statement"