Hi Glen,

Sorry for the delay in response.

> And how do I limit selections in an input drop down to just my specific file 
> type?  I'm guessing I need to extend the Tabular class, but I don't need to 
> add any additional functionality at this point, I just want to limit how the 
> tools can be chained together. 


We added the ability to dynamically create subclasses in changeset 
5176:34d3fcd8037b, by adding subclass="True" to the datatypes_conf.xml file. 
But your guess is correct, before this change you would need to have created a 
dummy do-nothing class.

> when I load data with this tool the format is set to "tabular" by galaxy and 
> not to my custom type.  I have a  feeling Galaxy is ignoring what the tool 
> .xml says the format of the output is and tries to autodetect, and comes up 
> with tabular.  If a data source says the output is a specific type shouldn't 
> galaxy use that as the format rather than autodetect?


There is a lot of legacy magic going on with datatype detection in datasource 
tools. We're currently working on cleaning this up and making it behave more 
sanely (e.g. make better use of the provided format attribute of the output 
dataset).  However, the preferred method of setting the datatype in datasource 
tools is to provide a 'data_type' parameter to Galaxy. If the datasource cannot 
provide this information, you can have Galaxy create it by providing a 
request_param_translation --> request_param tag set in the configuration .xml 
file for the datasource tool. An example:
        <request_param_translation>
            <request_param galaxy_name="data_type" remote_name="data_type" 
missing="my_datatype" />
        </request_param_translation>

Please let us know if we can provide additional information or help in any 
other way. Sorry again for the delay.


Thanks for using Galaxy,

Dan


On Feb 23, 2011, at 3:00 PM, Glen Beane wrote:

> I've created a custom file type based on the Galaxy Tabular type  (this is so 
> some tools I'm developing can declare this type as input or output and 
> prevent any arbitrary tabular file from being used as input for a tool)
> 
> I have a data source tool that declares its output format to be my type (this 
> tool brings the user to a website where they query a database and then sends 
> the data file back to galaxy)
> 
> when I load data with this tool the format is set to "tabular" by galaxy and 
> not to my custom type.  I have a  feeling Galaxy is ignoring what the tool 
> .xml says the format of the output is and tries to autodetect, and comes up 
> with tabular.  If a data source says the output is a specific type shouldn't 
> galaxy use that as the format rather than autodetect?
> 
> Also,  I have other tools that declare my type as the input type, yet when I 
> go to select an input file it shows me all tabular files in my history, not 
> just those with my custom type.
> 
> 
> how do I get the format to be correctly set for a file I load from my 
> data_source tool?  And how do I limit selections in an input drop down to 
> just my specific file type?  I'm guessing I need to extend the Tabular class, 
> but I don't need to add any additional functionality at this point, I just 
> want to limit how the tools can be chained together. This datatype is 
> probably just a place holder for what will probably end up being a binary 
> type, so I'm not going to put much effort in. 
> 
> 
> --
> Glen L. Beane
> Software Engineer
> The Jackson Laboratory
> Phone (207) 288-6153
> 
> 
> 
> 
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