It appears that you are attempting to directly name the output files. Instead, use a variable naming method that permits Galaxy to actually name the files accessed by the database, using <output> with <data> tags to link any working files (with "from_work_dir") and attach attributes (including metadata such as "format").
This section and the next is where in the Tool Config wiki you'll most likely want to start a review: https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax#A.3Coutputs.3E_t...
If you need a new datatype, this is the wiki that explains how to define one: https://wiki.galaxyproject.org/Admin/Datatypes/Adding%20Datatypes
Hopefully this helps,
Jen Galaxy team
On 4/3/14 5:13 AM, ANGELICA GOMEZ ROIG wrote:
I have made a wrapper that has a tool that giving it an input file, gives you two output files with known extension: .gem and .log I call the tool with a python file, and I pass it the input file and the two output file names for galaxy to show them, but when I look into de database/files/000/ i get four files: dataset_54.dat (my first declared output that it's empty) dataset_54.dat.gem (the output that throws the tool) dataset_54.dat.log (the other output file that throws the tool) dataset_55.dat (my second declared output that it's empty) So,what I'm getting in the galaxy interface is _54.dat and _55.dat, both empty, instead of _54.dat.gem and _54.dat.log that are the good ones. How can I fix these? Thanks
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/