YML File Usage

Example 1:

ConvertXFM:
  output_requirements:
    out_file: [in_file]
  output_templates:
    out_file: [ConvertXFM_output]
  doctest:
    in_file: flirt.mat
    invert_xfm: True
    out_file: flirt_inv.mat
    cmdline: convert_xfm -omat flirt_inv.mat -inverse flirt.mat
  tests_inputs:
    - in_file: flirt.mat
      invert_xfm: True
  tests_outputs:
    - out_file

Example 2

GLM:
  output_requirements:
    out_file: [in_file]
  output_callables:
  output_templates:
    out_file: "{in_file}_glm"
  inputs_drop:
  doctest:
    in_file: test.nii.gz
    design: confounds_regressors.tsv
    cmdline: fsl_glm -i test.nii.gz -d confounds_regressors.tsv -o test_glm.nii.gz
  tests_inputs:
    - in_file: test.nii.gz
      design: confounds_regressors.tsv
  tests_outputs:
    - out_file

output_requirements

• all outputs need to be listed here, even if you are not sure about their requirements. The converter.py needs the name here to generate output_fields

output_templates vs. output_callables

• if the output field has its input counterpart, use output_templates. For example, FSL sometimes requires out_file names in the input field. Otherwise, use output_callables.
• output_templates can be a function or a string; output_callables can only be a function.
• output_templates will use the same file extension and file path as the default setting; output_callables can allow you to change file extension and requires absolute file path specified.
• output_templates requires the field as str; output_callables requires the field as File, MultiOutputFile, or MultiOutputObj soon)