> Question: How save is the optional attribute ? I mean how consequent are
> you in this matter when the tool definition xml is to be created.

It's not clear to me what you're asking. That said, it's important to 
distinguish between Galaxy tool wrappers and their corresponding tools. Either 
deliberately or inadvertently, the wrapper may have different behavior than the 
tool. For example, an optional tool parameter may not be optional in the Galaxy 
wrapper because the wrapper author believes that explicitly setting a value is 

> Is
> there any relation to the conditional tag ?

No relation, but there can certainly be some confusion between conditional and 
optional parameters. It's not clear what the best way to solve this issue is.

> Another question: Have you ever thought about pipes. It seems that the
> tool xml schema entirely ignores it. For instance one could easily tag
> an input parameter to be able to read from stdin or to write to
> stdout/stderr. Especially samtools and bedtools do support pipes. Is
> there an obvious reason not to use it ?

Galaxy's treats each tool run autonomously right now; e.g., each tool run is 
submitted to the cluster as a separate job. This approach prevents pipes from 
being used. However, we are definitely interested in extending Galaxy to 
support piping in the future.

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