Update shell script outputs to match the CWL output format

[vedran-kasalica]

Update shell script outputs to match the CWL output format. The script should contain the header and in case of missing tools it should just list the tools that are missing instead of creating a partial script.

[eladrion]

If I see that correctly, APE does neither

1. contain shell scripts in the code base nor
2. generate shell scripts (it only generates CWL files and SnakeMake files).

So I close this issue. @vedran-kasalica Feel free to reopen and give an explanation, if that issue is actually still valid.

[eladrion]

This issue is seemingly about the shell scripts that can be enabled in the config.json, so I reopened again.