CPAT tool options

[SaimMomin12]

Request on behalf of our Galaxy user

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Dear Galaxy Europe team,

I recently found out that the usegalaxy.eu http://usegalaxy.eu/ server has the tool CPAT (link: https://usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/bgruening/cpat/cpat/3.0.5+galaxy0 https://usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/bgruening/cpat/cpat/3.0.5+galaxy0 ) available. This is a tool I had previously used online so this is very helpful for me (the online version only allows <10 MB files, while mine are larger). However, it looks like there is a problem with the interface/options for running this tool.

The first option (Query Nucleotides) allows FASTA files similar to the online version, but everything else requires files from the history for things like the reference genome. Is it possible to include an option to use data already included in Galaxy for this? i.e. to allow using the included hg19 genome, transcripts, CDS, etc. that I've seen other tools use?

Also, the default version of the CPAT tool published online (link: https://wlcb.oit.uci.edu/cpat/ https://wlcb.oit.uci.edu/cpat/ ) includes an option to just upload your transcript sequences as FASTA files, without any additional files for known CDS. I don't know if their site has the human reference genome already included, but it would be nice if I can do something similar in Galaxy.

Thank you for any help you can provide.

Sincerely, Pavel Vlasov, Columbia University Biological Sciences

[SaimMomin12]

• [x] Add an option to use reference either from history or in built reference