custom datatypes

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custom datatypes

Calvin Morrison
Hi,

I just want a simple data type for my 'custom' datatype (it's just a trained matrix in a specific format generated by my database building tool), so that my tools which use this database will only see ones with that format in the dropdown select list.

in my datatypes.xml i have this:

<datatype extension="gz" type="galaxy.datatypes.quikrdb" mimetype="application/octet-stream" display_in_upload="true" description="A database trained with quikr." />

then in my tool xml files i have


<outputs>
  <data name="output" format="quikrdb" />
</outputs>

which seems to be fine, but my tools which use it still show me all my data, not just trained db's

<param name="dbname" type="data" format="quikrdb" label="custom trained database"/>

Am i doing something wrong?

Calvin Morrison

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Re: custom datatypes

Peter Cock
Hi Calvin,

The "extension" is really the Galaxy datatype name, so
put "quikrdb" here. The actual filename on disk will be *.dat
once loaded into Galaxy.

More examples, e.g.
https://github.com/peterjc/galaxy_blast/blob/master/datatypes/blast_datatypes/datatypes_conf.xml

Peter

On Fri, Sep 12, 2014 at 9:40 PM, Calvin Morrison <[hidden email]> wrote:

> Hi,
>
> I just want a simple data type for my 'custom' datatype (it's just a trained
> matrix in a specific format generated by my database building tool), so that
> my tools which use this database will only see ones with that format in the
> dropdown select list.
>
> in my datatypes.xml i have this:
>
> <datatype extension="gz" type="galaxy.datatypes.quikrdb"
> mimetype="application/octet-stream" display_in_upload="true" description="A
> database trained with quikr." />
>
> then in my tool xml files i have
>
>
> <outputs>
>   <data name="output" format="quikrdb" />
> </outputs>
>
> which seems to be fine, but my tools which use it still show me all my data,
> not just trained db's
>
> <param name="dbname" type="data" format="quikrdb" label="custom trained
> database"/>
>
> Am i doing something wrong?
>
> Calvin Morrison
>
> ___________________________________________________________
> Please keep all replies on the list by using "reply all"
> in your mail client.  To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
>   http://lists.bx.psu.edu/
>
> To search Galaxy mailing lists use the unified search at:
>   http://galaxyproject.org/search/mailinglists/
___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
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