Datatype for binning files


I just started to work on the wrapper for cami-amber. After reading what kind of data types I need, I discovered that there is no datatype in galaxy/lib/galaxy/config/sample/datatypes_conf.xml.sample at dev · galaxyproject/galaxy · GitHub for binning files so which kind of type should I enter in the wrapper now? Also, which kind of datatype I use when there is no extension for a file? Both example are here in this image for better understanding.

Thanks for the help!

Welcome, @SantaMcCloud

You can create/define new datatypes as needed. If you plan on publishing the tool wrapper to the Tool Shed, and want to try to get it hosted a public Galaxy servers, I would suggest coordinating with the IUC or the Backend group → Galaxy Working Groups - Galaxy Community Hub

Datatypes are “sniffed” meaning “guessed” during Upload. It can be annoying as a user to have the wrong datatype guessed so keep that in mind. Also remember that datatypes can overlap or nest: A bed file is a more specific type of tabular file, and all tabular files are also plain text. The default if there is no way to assign a datatype is “data” (a fall back that tells you nothing about the content – not even if compressed or not).

Docs with more → Search — Galaxy Project 24.0.1.dev0 documentation

Thank you for the answer tabular, as the format works fine. I also test the tool with .tsv file, and it does also work with it!

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Great choice! Thanks for posting back what will work.

tabular is a very flexible datatype: any tsv file (tab-seperated-values) should be autodetected by the Upload tool as “tabular”, and most of the text manipulation tools will work too (in case anything needs to be adjusted by the user).

I’m sure you know all of this – just clarifying for readers later on who might find the topic :slight_smile: