How to create an OSX Application to wrap a call to a shell script?
I can see a couple of things wrong there.

Firstly you have opened a workflow and not an Application.

You should choose Application when you make your selection for the type of Automator file.



And the code you have will not work as you expect, since you have not changed directory. (cd).

In the code as you have it, all it is doing is getting the path as an alias and storing it in the variable  current_path and in a format unsuitable for the unix commands.

But you do not use it.

So the current directory will most likely be your home folder

At this stage there is no telling what it is trying to launch.

If I run it as you have it I get.



Which makes sense since I do not have Java installed. But if I did I would not expect it to find the right file.

The Applescript need to look like this.

on run {input, parameters}
    tell application "Finder"
        set current_path to container of (path to me) as alias
    end tell

    do shell script "cd " &amp; quoted form of (POSIX path of current_path) &amp; " ;ls | open -fe"

    return input
end run 


In my example

do shell script "cd " &amp; quoted form of (POSIX path of current_path) &amp; " ;/bin/ls | /usr/bin/open -fe"


I cd to the POSIX path of the alias in the  variable  current_path 

i.e from "alias "Macintosh HD:Applications:""   to  "/Applications/"

The quoted form of  escapes the path using quotes.

I have used the /bin/ls command and pipe it to the open in TextEdit stdin as a demonstration here so that you can test to see if you are getting to the area you expect.

You would use something like;

do shell script "cd " &amp; quoted form of (POSIX path of current_path) &amp; " ;\"java -jar app.jar\""




update:

A another way is just use pure Applescript.

on run {input, parameters}
    tell application "Finder"
        set current_path to container of (path to me)

        set theFile to (current_path) as alias

        open file "java -jar app.jar" of theFile
    end tell


end run