FIX: Improve output handling in DWIDenoise and DWIBiasCorrect

[josephmje]

Summary

Fixes #2975 .

List of changes proposed in this PR (pull-request)

• DWIDenoise
  • use name_template to auto-generate noise file
  • remove _list_outputs() method
• MRDeGibbs
  • remove use_default=True so that values can be changed
• DWIBiasCorrect
  • recycle grad_file and grad_fsl from MRTrix3Base spec and add xor since arguments are mutually exclusive
  • remove min_version=5.0.10 since the Mrtrix3 version is being checked, not FSL
  • remove _list_outputs() method

Acknowledgment

• (Mandatory) I acknowledge that this contribution will be available under the Apache 2 license.

[josephmje]

@oesteban I was wondering if I could get your feedback on this fix? Thank you!

[effigies]

Overall looks good. Some comments.

Also:

remove use_default=True so that values can be changed

usedefault=True does not prevent overriding.

[codecov-io]

Codecov Report

Merging #2978 into master will increase coverage by 0.01%.
The diff coverage is 100%.

@@            Coverage Diff             @@
##           master    #2978      +/-   ##
==========================================
+ Coverage   67.61%   67.62%   +0.01%     
==========================================
  Files         344      344              
  Lines       43798    43782      -16     
  Branches     5471     5469       -2     
==========================================
- Hits        29612    29606       -6     
+ Misses      13475    13465      -10     
  Partials      711      711

Flag	Coverage Δ
#smoketests	50.38% <ø> (ø)	⬆️
#unittests	65.04% <100%> (+0.01%)	⬆️

Impacted Files	Coverage Δ
nipype/interfaces/mrtrix3/base.py	56.36% <ø> (ø)	⬆️
nipype/interfaces/mrtrix3/preprocess.py	86.59% <100%> (+6.95%)	⬆️

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[effigies]

It's usedefault, not use_default. And one other comment.

[effigies]

LGTM.