Obitools first version

[yvanlebras]

Hi GTN!

A first draft version of Obitools eDNA / metabarcoding tutorial, from this history: https://ecology.usegalaxy.eu/u/ylebras/h/tuto-obitools

[hexylena]

It's fine if they don't have a github username, if they don't just put github: false when you add them to the CONTRIBUTORS.yaml (and make up a 'username' for them.)

[hexylena]

c'est vert!! Wonderful!

[yvanlebras]

Hey hey! It appears to me I adressed all comments, thank you so much Anne, Cristobal !!!!

[yvanlebras]

it appears I have an issue with an URL:

(https://pythonhosted.org/OBITools/welcome.html) is an invalid URL

Any idea @hexylena ? Do you think we an merge afterthat?

[hexylena]

Suggested change

The OBITools commands consider a sequence record as an entity composed of five distinct elements. Two of them are mandatory, the identifier (id) and the DNA or protein sequence itself. The id is a single word composed of characters, digits, and other symbols like dots or underscores excluding spaces. Formally, the ids should be unique within a dataset and should identify each sequence record unambiguously, but only a few OBITools actually rely on this property. The three other elements composing a sequence record are optional. They consist in a sequence definition, a quality vector, and a set of attributes. The last element is a set of attributes qualifying the sequence, each attribute being described by a key=value pair. The set of attributes is the central concept of the OBITools system. When an OBITools command is run on the sequence records included in a dataset, the result of the computation often consist in the addition of new attributes completing the annotation of each sequence record. This strategy of sequence annotation allows the OBITools to return their results as a new sequence record file that can be used as the input of another OBITools program, ultimately creating complex pipelines (source: [(https://pythonhosted.org/OBITools/welcome.html)]((https://pythonhosted.org/OBITools/welcome.html))).

The OBITools commands consider a sequence record as an entity composed of five distinct elements. Two of them are mandatory, the identifier (id) and the DNA or protein sequence itself. The id is a single word composed of characters, digits, and other symbols like dots or underscores excluding spaces. Formally, the ids should be unique within a dataset and should identify each sequence record unambiguously, but only a few OBITools actually rely on this property. The three other elements composing a sequence record are optional. They consist in a sequence definition, a quality vector, and a set of attributes. The last element is a set of attributes qualifying the sequence, each attribute being described by a key=value pair. The set of attributes is the central concept of the OBITools system. When an OBITools command is run on the sequence records included in a dataset, the result of the computation often consist in the addition of new attributes completing the annotation of each sequence record. This strategy of sequence annotation allows the OBITools to return their results as a new sequence record file that can be used as the input of another OBITools program, ultimately creating complex pipelines (source: [OBITools Welcome](https://pythonhosted.org/OBITools/welcome.html)).

I think the double () was the issue, and yes, we can merge after this!! Amazing work @yvanlebras

[hexylena]

Congrats @yvanlebras et al!

[bgruening]

🎉

[yvanlebras]

AMAZING!!! THANK YOU SOME MUCH ;) Helena ! Saskia ! Galaxy-E team !!! All !!!!!!!!