Add Fairy

[SantaMcCloud]

FOR CONTRIBUTOR:

• I have read the CONTRIBUTING.md document and this tool is appropriate for the tools-iuc repo.
• License permits unrestricted use (educational + commercial)
• This PR adds a new tool or tool collection
• This PR updates an existing tool or tool collection
• This PR does something else (explain below)

[SantaMcCloud]

I know that there will be an error because of the format bcsp. Is it possible to add this format into the galaxy datatype?

I can do it but i have to read and maybe ask question about it. I tried to use the tabular format but with this the tool had always erros possible because the bcsp is a binary file.

[SantaMcCloud]

i also get this error when i try to test fairy_cov.xml

(planemo) (fairy_env) sf373@LAPTOP-7RMLPR2D:~/sf373$ planemo test tools-iuc/tools/fairy/fairy_cov.xml 
Traceback (most recent call last):
  File "/home/sf373/sf373/planemo/bin/planemo", line 8, in <module>
    sys.exit(planemo())
  File "/home/sf373/sf373/planemo/lib/python3.7/site-packages/click/core.py", line 1157, in __call__
    return self.main(*args, **kwargs)
  File "/home/sf373/sf373/planemo/lib/python3.7/site-packages/click/core.py", line 1078, in main
    rv = self.invoke(ctx)
  File "/home/sf373/sf373/planemo/lib/python3.7/site-packages/click/core.py", line 1688, in invoke
    return _process_result(sub_ctx.command.invoke(sub_ctx))
  File "/home/sf373/sf373/planemo/lib/python3.7/site-packages/click/core.py", line 1434, in invoke
    return ctx.invoke(self.callback, **ctx.params)
  File "/home/sf373/sf373/planemo/lib/python3.7/site-packages/click/core.py", line 783, in invoke
    return __callback(*args, **kwargs)
  File "/home/sf373/sf373/planemo/lib/python3.7/site-packages/click/decorators.py", line 92, in new_func
    return ctx.invoke(f, obj, *args, **kwargs)
  File "/home/sf373/sf373/planemo/lib/python3.7/site-packages/click/core.py", line 783, in invoke
    return __callback(*args, **kwargs)
  File "/home/sf373/sf373/planemo/lib/python3.7/site-packages/planemo/cli.py", line 103, in handle_blended_options
    return f(*args, **kwds)
  File "/home/sf373/sf373/planemo/lib/python3.7/site-packages/planemo/commands/cmd_test.py", line 76, in cli
    return_value = test_runnables(ctx, runnables, original_paths=uris, **kwds)
  File "/home/sf373/sf373/planemo/lib/python3.7/site-packages/planemo/engine/test.py", line 13, in test_runnables
    test_data = engine.test(runnables, test_timeout=kwds.get("test_timeout"))
  File "/home/sf373/sf373/planemo/lib/python3.7/site-packages/planemo/engine/interface.py", line 79, in test
    test_cases = [t for tl in map(cases, runnables) for t in tl]
  File "/home/sf373/sf373/planemo/lib/python3.7/site-packages/planemo/engine/interface.py", line 79, in <listcomp>
    test_cases = [t for tl in map(cases, runnables) for t in tl]
  File "/home/sf373/sf373/planemo/lib/python3.7/site-packages/planemo/runnable.py", line 261, in cases
    test_dicts = tool_source.parse_tests_to_dict()
  File "/home/sf373/sf373/planemo/lib/python3.7/site-packages/galaxy/tool_util/parser/xml.py", line 649, in parse_tests_to_dict
    tests.append(_test_elem_to_dict(test_elem, i, profile))
  File "/home/sf373/sf373/planemo/lib/python3.7/site-packages/galaxy/tool_util/parser/xml.py", line 693, in _test_elem_to_dict
    outputs=__parse_output_elems(test_elem),
  File "/home/sf373/sf373/planemo/lib/python3.7/site-packages/galaxy/tool_util/parser/xml.py", line 718, in __parse_output_elems
    name, file, attributes = __parse_output_elem(output_elem)
  File "/home/sf373/sf373/planemo/lib/python3.7/site-packages/galaxy/tool_util/parser/xml.py", line 728, in __parse_output_elem
    file, attributes = __parse_test_attributes(output_elem, attrib, parse_discovered_datasets=True)
  File "/home/sf373/sf373/planemo/lib/python3.7/site-packages/galaxy/tool_util/parser/xml.py", line 781, in __parse_test_attributes
    attributes["object"] = json.loads(attrib.pop("value_json"))
  File "/home/sf373/anaconda3/envs/comebin_env/lib/python3.7/json/__init__.py", line 348, in loads
    return _default_decoder.decode(s)
  File "/home/sf373/anaconda3/envs/comebin_env/lib/python3.7/json/decoder.py", line 337, in decode
    obj, end = self.raw_decode(s, idx=_w(s, 0).end())
  File "/home/sf373/anaconda3/envs/comebin_env/lib/python3.7/json/decoder.py", line 355, in raw_decode
    raise JSONDecodeError("Expecting value", s, err.value) from None
json.decoder.JSONDecodeError: Expecting value: line 1 column 1 (char 0)

I dont know how this error happen but i will have a look at this the next couple of days. Maybe i can fix it somehow

[bernt-matthias]

I know that there will be an error because of the format bcsp. Is it possible to add this format into the galaxy datatype?

Yes. Is they documentation available?

[bernt-matthias]

I dont know how this error happen but i will have a look at this the next couple of days. Maybe i can fix it somehow

I think value_json="normal_test.tsv" should be value="normal_test.tsv".

[SantaMcCloud]

I know that there will be an error because of the format bcsp. Is it possible to add this format into the galaxy datatype?

Yes. Is they documentation available?

Yes and i found the right tab to it. I will read it and try it out!

[SantaMcCloud]

I dont know how this error happen but i will have a look at this the next couple of days. Maybe i can fix it somehow

I think value_json="normal_test.tsv" should be value="normal_test.tsv".

yes i didnt saw this typo yesterday thank you for the hint :)

[SantaMcCloud]

@bernt-matthias i have a question about adding a datatype. Do i have to add a sniffer or is this an optional function?

[SantaMcCloud]

galaxyproject/galaxy#19365