Misc updates for planemo dependency_script #545
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Also the output shell script names are still hard coded.
This was added for galaxyproject#404 but the commands are needlessly verbose.
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Closes #544 by implementing
target_filename.Tweaks change #537 for #404 which was too verbose.
Clarifies help.
Fixes another corner case when
$DOWNLOAD_CACHEwas not set.