Hello all,

Not sure if the mailing list or trello would be appropriate for this.
I had a problem using the gff_filter_by_attribute tool, both locally and on
Neither filtering for GTF or GFF were working.

The error message was:

Traceback (most recent call last):
  File "/home/galaxy/galaxy-dist/lib/galaxy/jobs/runners/__init__.py",
line 158, in prepare_job
  File "/home/galaxy/galaxy-dist/lib/galaxy/jobs/__init__.py", line
832, in prepare
    self.command_line, self.extra_filenames = tool_evaluator.build()
  File "/home/galaxy/galaxy-dist/lib/galaxy/tools/evaluation.py", line
408, in build
    self.__build_command_line( )
  File "/home/galaxy/galaxy-dist/lib/galaxy/tools/evaluation.py", line
424, in __build_command_line
    command_line = fill_template( command, context=param_dict )
  File "/home/galaxy/galaxy-dist/lib/galaxy/util/template.py", line 9,
in fill_template
    return str( Template( source=template_text, searchList=[context] ) )
line 1004, in __str__
    return getattr(self, mainMethName)()
  File "DynamicallyCompiledCheetahTemplate.py", line 92, in respond
NotFound: cannot find 'attribute_types' while searching for

I could fix it by importing safe_dumps from galaxy.util.json, which
apparently was not imported.
The next problem occurred because gff_filter_by_attribute expects GTF
attribute name-value separators (" ") but allowed GFF input, which uses
("=") as separator. I added a logic to switch
between seperators based on the file extension. Everything works smoothly
the code changes are here:
Should I create a pull request?

Marius van den Beek, PhD

Drosophila Genetics and Epigenetics
Institut de Biologie Paris Seine
9, Quai St Bernard, BoƮte courrier 24
75252 Paris Cedex 05
Tel +33 01 44 27 34 01
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