Question: Difference Between a Python Tool vs. Wrapper
2
gravatar for rlee03
2.8 years ago by
rlee0350
United States
rlee0350 wrote:

What is the difference between the Wrapper and the Tools? Please be explicit.

I have a limited background in comp sci and galaxy. Can you reference the folders in galaxy-dist in your explanation and also give an example?

Making the connection between the GUI and folders and python files will clear this up. Thanks!

tool python wrapper • 865 views
ADD COMMENTlink modified 2.8 years ago by Martin Čech ♦♦ 4.3k • written 2.8 years ago by rlee0350
2
gravatar for Martin Čech
2.8 years ago by
Martin Čech ♦♦ 4.3k
United States
Martin Čech ♦♦ 4.3k wrote:

Let there be a sequence processing tool written by Heng Li that is called seqtk (https://github.com/lh3/seqtk).

Then if we want to use this tool in Galaxy we have to write a wrapper that will wrap the tool and display it in the Galaxy's interface. This wrapper is in the form of an XML file and is commonly referred to as Galaxy Tool, wrapper, and sometimes even toolconf. It describes to Galaxy how to call the underlying tool (the seqtk) and how to connect the inputs/outputs. The underlying tool can be written in any language.
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Let there be a very complicated tool that is called htseq.

Then if we want to use it in Galaxy we could find that the XML syntax for wrapper is not capable enough to do what we want. We will decide to write a Python wrapper for it as Python can express our needs. This Python wrapper will wrap the htseq tool exposing inputs and outputs. It can be written in any language. Afterwards we still have to create the Galaxy Tool in the form of XML but this time, the Galaxy Tool will call the Python wrapper which in turn calls the underlying htseq.
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The actual seqtk XML wrappers can be found here: https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk
The actual htseq XML wrappers can be found here: https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq

Thank you for using Galaxy. Let me know if you have any questions

Martin

 

ADD COMMENTlink modified 2.8 years ago • written 2.8 years ago by Martin Čech ♦♦ 4.3k
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