Hi Marius,

It'd be great if you wanted to submit a PR for the json issue separately -- I can confirm that that's a working fix.  I'll let someone else speak to the tool change.

-Dannon

On Thu, Apr 30, 2015 at 2:30 PM Marius van den Beek <m.vandenbeek@gmail.com> wrote:

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 usegalaxy.org.

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
    job_wrapper.prepare()
  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] ) )
  File "/home/galaxy/galaxy-dist/eggs/Cheetah-2.2.2-py2.7-linux-x86_64-ucs4.egg/Cheetah/Template.py", line 1004, in __str__
    return getattr(self, mainMethName)()
  File "DynamicallyCompiledCheetahTemplate.py", line 92, in respond
NotFound: cannot find 'attribute_types' while searching for 'input.metadata.attribute_types'

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 now,

the code changes are here:

https://github.com/mvdbeek/galaxy

Should I create a pull request?

--

Marius van den Beek, PhD

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

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