Just to summarize what I found about getting tool parameter <param 
type="library_data" > going again (though a future expansion of dataset 
parameters to handle this would be great, esp. if one can specify a particular 
data library):

1) Aysam's patch (thanks!)
2) Tool_form.mako has a hardcoded url that doesn't work for galaxy installs 
that have a prefix so that needs adjustment:

  $(".add-librarydataset").click(function() {
                var link = $(this);
                    url: "/visualization/list_libraries",

Now one gets the popup form in one's tool where one or more library datasets 
can be selected.  Selecting one or more gets them listed in one's tool form.

However, I'm not understanding how to get those items submitted with galaxy 
form <command> params.  I tried for example:
  -B "$library_datasets[0].file_name"
and also tried a loop to enumerate the dataset file names.

I keep on getting: 

File "cheetah_DynamicallyCompiledCheetahTemplate_1421706558_2_37415.py", line 
203, in respond
TypeError: object of type 'LibraryDatasetValueWrapper' has no len()

If anyone knows the solution, that would be appreciated.


Hsiao lab, BC Public Health Microbiology & Reference Laboratory, BC Centre for 
Disease Control
655 West 12th Avenue, Vancouver, British Columbia, V5Z 4R4 Canada
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