Add ckeck-tools option for correcting tool XML command.

phnmnl / container-galaxy-k8s-runtime

PhenoMeNal runtime for Galaxy running inside a container orchestrator

Apache License 2.0

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Add ckeck-tools option for correcting tool XML command. #327

Open pkrog opened 5 years ago

pkrog commented 5 years ago

A new option (--correct-command) in check-tools script allows to remove automatically the use of $__tool_directory__ macro inside the command tag of XML tool files. The use of that command prevents the tool's container from running in Galaxy/Kubernetes.

ilveroluca commented 5 years ago

I totally agree flagging $__tool_directory__ as a problem when found. Maybe automatically editing the file is a little too ambitious? Would the code would be able to ensure the edited path is indeed valid?