started to manual touch up auto-conv yaml specs

nipype-auto-conv/specs/accuracy_tester.yaml

@@ -25,9 +25,9 @@ inputs:
   # passed to the field in the automatically generated unittests.
     trained_wts_file: generic/file
     # type=file|default=<undefined>: trained-weights file
-    mel_icas: generic/directory+list-of
+    mel_icas: medimage-fsl/melodic-ica+list-of
     # type=inputmultiobject|default=[]: Melodic output directories
-    output_directory: generic/directory
+    output_directory: Path
     # type=directory: Path to folder in which to store the results of the accuracy test.
     # type=directory|default=<undefined>: Path to folder in which to store the results of the accuracy test.
   metadata:

nipype-auto-conv/specs/apply_mask.yaml

@@ -20,9 +20,9 @@ inputs:
   # from the nipype interface, but you may want to be more specific, particularly
   # for file types, where specifying the format also specifies the file that will be
   # passed to the field in the automatically generated unittests.
-    mask_file: generic/file
+    mask_file: medimage/nifti-gz
     # type=file|default=<undefined>: binary image defining mask space
-    in_file: generic/file
+    in_file: medimage/nifti-gz
     # type=file|default=<undefined>: image to operate on
   metadata:
   # dict[str, dict[str, any]] - additional metadata to set on any of the input fields (e.g. out_file: position: 1)
@@ -37,15 +37,15 @@ outputs:
   # from the nipype interface, but you may want to be more specific, particularly
   # for file types, where specifying the format also specifies the file that will be
   # passed to the field in the automatically generated unittests.
-    out_file: generic/file
+    out_file: medimage/nifti-gz
     # type=file: image written after calculations
     # type=file|default=<undefined>: image to write
   callables:
   # dict[str, str] - names of methods/callable classes defined in the adjacent `*_callables.py`
   # to set to the `callable` attribute of output fields
   templates:
   # dict[str, str] - `output_file_template` values to be provided to output fields
-    out_file: out_file
+    out_file: out_file.nii.gz
     # type=file: image written after calculations
     # type=file|default=<undefined>: image to write
   requirements:

nipype-auto-conv/specs/apply_warp.yaml

@@ -33,17 +33,17 @@ inputs:
   # from the nipype interface, but you may want to be more specific, particularly
   # for file types, where specifying the format also specifies the file that will be
   # passed to the field in the automatically generated unittests.
-    in_file: generic/file
+    in_file: medimage/nifti-gz
     # type=file|default=<undefined>: image to be warped
-    ref_file: generic/file
+    ref_file: medimage/nifti-gz
     # type=file|default=<undefined>: reference image
-    field_file: generic/file
+    field_file: medimage/nifti-gz
     # type=file|default=<undefined>: file containing warp field
-    premat: generic/file
+    premat: Path
     # type=file|default=<undefined>: filename for pre-transform (affine matrix)
-    postmat: generic/file
+    postmat: Path
     # type=file|default=<undefined>: filename for post-transform (affine matrix)
-    mask_file: generic/file
+    mask_file: Path
     # type=file|default=<undefined>: filename for mask image (in reference space)
   metadata:
   # dict[str, dict[str, any]] - additional metadata to set on any of the input fields (e.g. out_file: position: 1)