Repeatexplorer

[TomHarrop]

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[TomHarrop]

I've done this to avoid all the cp commands in the original wrapper, but I think this means it's writing directly to the output directory? Let me know if there's a better way to pick up the additional content for the html file.

galaxy-tools/tools/repeatexplorer2/repex_full_clustering.xml

Line 22 in 983e4b3

--output_dir=${ReportFile.extra_files_path}

[bgruening]

I've done this to avoid all the cp commands in the original wrapper, but I think this means it's writing directly to the output directory? Let me know if there's a better way to pick up the additional content for the html file.

galaxy-tools/tools/repeatexplorer2/repex_full_clustering.xml

Line 22 in 983e4b3

--output_dir=${ReportFile.extra_files_path}

I guess that's fine if really ALL files are needed in this HTML output. If not the cp or mv might actually a more explicit way to do.

[TomHarrop]

I've done this to avoid all the cp commands in the original wrapper, but I think this means it's writing directly to the output directory? Let me know if there's a better way to pick up the additional content for the html file.

galaxy-tools/tools/repeatexplorer2/repex_full_clustering.xml

Line 22 in 983e4b3

--output_dir=${ReportFile.extra_files_path}

I guess that's fine if really ALL files are needed in this HTML output. If not the cp or mv might actually a more explicit way to do.

Yep. I doubt they are all needed but I don't think it will be quick to work out exactly which ones are.

[bgruening]

Can you convert that to a suite of tools?
In the original repo there have been two tools at least isn't it?

[TomHarrop]

I converted it to a suite.

BTW @bgruening it looked to me like the second wrapper runs the same command as the first with an additional option tarean_mode, so we can just include that function in this wrapper if we want it.

[TomHarrop]

(probably)

[bgruening]

Yes, lets do that then. In general a suite can not hurt, so its fine to have it as suite in case we ever want to extend it. Thanks

[bgruening]

can we keep the names all lower case?

[bgruening]

add min=2?

[bgruening]

Thanks @TomHarrop