Question: How to access user preferences from inside tool XML
gravatar for christopherbare
3.9 years ago by
United States
christopherbare10 wrote:

I defined a form using Admin | Form Definitions | Manage form definitions, which contains settings for a tool. Now, I'm wondering if I can access that my the Galaxy Tool XML File.

What I'm hoping to do is fill in defaults settings for the tool's parameters and include an API key for accessing a remote web service that requires a login

The genomespace tool does something like this with OpenID credentials:

#set $username = $__user__.preferences.get( 'genomespace_username', None )
#set $token = $__user__.preferences.get( 'genomespace_token', None )

But, I'd like to do it with the User Information form, if possible. Any hints?


tool galaxy • 879 views
ADD COMMENTlink modified 3.8 years ago • written 3.9 years ago by christopherbare10
gravatar for christopherbare
3.8 years ago by
United States
christopherbare10 wrote:

Cool, this does work. The command section of my galaxy tool XML file looks something like this:

  <command interpreter="python">
    --html "$html_outfile"
    #set $param_a = $__user__.values.content.get( 'my_app_param_a', None )
    #set $param_b = $__user__.values.content.get( 'my_app_param_b', None )
    --a "${param_a}"
    --b "${param_b}"


ADD COMMENTlink written 3.8 years ago by christopherbare10

Glad you figured this out, and thanks for following up with a way to do it!

ADD REPLYlink written 3.8 years ago by Dannon Baker3.7k
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