[WIP] Initial Galaxy support

[blankenberg]

No description provided.

[multimeric]

Let me know when this is ready for review or when you want to hand this over to me if you can't finish it.

[bernt-matthias]

I'm also available for helping if needed.

[multimeric]

@bernt-matthias if you have some spare time and think you can finish this off, I would certainly appreciate it. Otherwise it may not get into a release for a while.

[bernt-matthias]

Hi @TMiguelT .

• Do you have examples for CliEnum, CliList, CliTuple?
• Is there some way to obtain the (conda) package name and the version?
• The outputs todo of @blankenberg might be resolvable by an idea to guess if files / dirs are in / output #15
• Othewise I could start to implement the <command/> tag. Which is I guess the most work.
• I guess we also need to extend tests. Where should I start... ?

[multimeric]

Do you have examples for CliEnum, CliList, CliTuple?

Do you mean examples of flags that should have this type?

• CliTuple: bwa mem -I FLOAT[,FLOAT[,INT[,INT]]]
• CliEnum: htseq-count --stranded {yes,no,reverse}
• CliList: bedtools multiinter -i FILE1 FILE2 .. FILEn.

Is there some way to obtain the (conda) package name and the version?

Not at this point. I'm happy to add some optional conda metadata to the tool definitions generated over in BiocondaAutomation, but you can't assume that it exists, because aCLImatise is an independent CLI tool. What do you need it for?

Otherwise I could start to implement the <command/> tag. Which is I guess the most work.

Didn't we work out that planemo generated the command for us?
Sidenote: a lot of my upstream changes are now merged so installing planemo alongside aCLImatise might be possible now

I guess we also need to extend tests. Where should I start... ?

If you just write a validation function for Galaxy XML that uses, say, Planemo, then I'm happy. If you want you can add some extra validations to this function, such as checking that all flags are present in the XML. Then that will automatically hook into my e2e test suite. You don't need to write Galaxy-specific tests