Question: Is it possible to add custom JavaScript tool in Galaxy
0
gravatar for JameB11
11 days ago by
JameB110
JameB110 wrote:

I'm looking into adding a custom tool into Galaxy that makes a HTTP request to an API end point, parses the response , and dynamically generates a form for the user. I want to do this using JavaScript and not serverside scripting languages like Python or Perl.

Is this something that could be done? I looked at the Add Custom Tool page, but it only talks about Perl/Python scripts. The front-end that user interacts with has to be defined using XML file ... I want to instead give my own HTML+CSS+JS file.

The form I'm generating dynamically allows users to generate data which can be used for further analysis. While I can't tell you exactly what it is (yet), a pseudo workflow could be:

  1. User comes on custom Galaxy instance
  2. Acquires data using the custom tool.
  3. The tool acquires form structure from the API
  4. Generates some genomic data, Galaxy would keep this in history
  5. User can perform some other analysis using the output in (4) ... i.e. say compute GC content, as a basic example.
galaxy • 51 views
ADD COMMENTlink modified 11 days ago by Martin Čech ♦♦ 3.7k • written 11 days ago by JameB110
1
gravatar for Martin Čech
11 days ago by
Martin Čech ♦♦ 3.7k
United States
Martin Čech ♦♦ 3.7k wrote:

Two things come to my mind when adding custom frontend JS to Galaxy, none of them are tools per se though.

Galaxy does not support normal tools written in javascript. Most tools are resource-intensive and wouldn't run well in browser. Moreover trying to load from a different domain's API through browser will trigger the same-origin security policy and browser would prevent that request.

ADD COMMENTlink written 11 days ago by Martin Čech ♦♦ 3.7k
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