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Unclear how exactly the user has done this, but this parameter definition
<param name="overlap_mode" type="select" multiple="true" label="What should be written to the output file?">
<option value="-wa">
Write the original entry in A for each overlap (-wa)
</option>
<option value="-wb">
Write the original entry in B for each overlap. Useful for knowing what A overlaps. Restricted by the fraction- and reciprocal option (-wb)
</option>
<option value="-wo">
Write the original A and B entries plus the number of base pairs of overlap between the two features. Only A features with overlap are reported. Restricted by the fraction- and reciprocal option (-wo)
</option>
<option value="-wao">
Write the original A and B entries plus the number of base pairs of overlap between the two features. However, A features w/o overlap are also reported with a NULL B feature and overlap = 0. Restricted by the fraction- and reciprocal option (-wao)
</option>
<option value="-loj">
Perform a "left outer join". That is, for each feature in A report each overlap with B. If no overlaps are found, report a NULL feature for B (-loj)
</option>
</param>
from bedtools intersect
led to:
TypeError: sequence item 0: expected str instance, NoneType found
File "galaxy/web/framework/decorators.py", line 346, in decorator
rval = func(self, trans, *args, **kwargs)
File "galaxy/webapps/galaxy/api/tools.py", line 247, in build
return tool.to_json(trans, kwd.get("inputs", kwd), history=history)
File "galaxy/tools/__init__.py", line 2509, in to_json
populate_state(request_context, self.inputs, params.__dict__, state_inputs, state_errors)
File "galaxy/tools/parameters/__init__.py", line 412, in populate_state
_populate_state_legacy(
File "galaxy/tools/parameters/__init__.py", line 625, in _populate_state_legacy
check_param(request_context, input, param_value, context, simple_errors=simple_errors)
File "galaxy/tools/parameters/__init__.py", line 246, in check_param
value = param.from_json(value, trans, param_values)
File "galaxy/tools/parameters/basic.py", line 1045, in from_json
f"invalid options ({','.join(set(value) - set(legal_values))!r}) were selected (valid options: {','.join(legal_values)})",
where value is
[None, '-wb']
I can partially fix this on the backend so that a proper error is returned, however this selection is wrong and needs to be fixed on the client.
The text was updated successfully, but these errors were encountered:
Unclear how exactly the user has done this, but this parameter definition
from bedtools intersect
led to:
where value is
I can partially fix this on the backend so that a proper error is returned, however this selection is wrong and needs to be fixed on the client.
The text was updated successfully, but these errors were encountered: