added more descriptive doc string

Author: tclose

example-specs/ants_registration_param.yml

@@ -0,0 +1,43 @@
+Registration:
+  output_requirements:
+    output_warped_image: ["fixed_image", "moving_image", "output_transform_prefix"]
+  output_templates:
+    output_warped_image: "{output_transform_prefix}warped"
+  doctest:
+    fixed_image: test.nii.gz
+    moving_image: test.nii.gz
+    cmdline: >- 
+      antsRegistration --output [ output_, output_warped_image.nii.gz ]
+      --metric Mattes[ test.nii, test.nii, 1, 32, Random, 0.05 ]
+  tests_inputs:
+    -
+  tests_outputs:
+    - AttributeError
+    
+
+# CopyGeom:
+#   output_requirements:
+#     out_file: [in_file, dest_file]
+#   output_templates:
+#     dest_file: "original"
+#     out_file: "{dest_file}"
+#   doctest:
+#     in_file: test.nii.gz
+#     dest_file: dest.nii.gz
+#     cmdline: fslcpgeom test.nii.gz dest.nii.gz
+#   tests_inputs:
+#     -
+
+#   tests_outputs:
+#     - AttributeError
+
+
+# Split:
+#   output_requirements:
+#     out_file: [in_file, dimension]
+#   output_templates:
+#   doctest:
+#   tests_inputs:
+#     -
+#   tests_outputs:
+#     - AttributeError

example-specs/ants_segmentation_param.yml

@@ -0,0 +1,42 @@
+N4BiasFieldCorrection:
+  output_requirements:
+    output_image: []
+    bias_image: ["save_bias"]
+  output_templates:
+    output_image: ""
+  doctest:
+    input_image: test.nii.gz
+    cmdline: 
+      
+  tests_inputs:
+    -
+  tests_outputs:
+    - AttributeError
+    
+
+# CopyGeom:
+#   output_requirements:
+#     out_file: [in_file, dest_file]
+#   output_templates:
+#     dest_file: "original"
+#     out_file: "{dest_file}"
+#   doctest:
+#     in_file: test.nii.gz
+#     dest_file: dest.nii.gz
+#     cmdline: fslcpgeom test.nii.gz dest.nii.gz
+#   tests_inputs:
+#     -
+
+#   tests_outputs:
+#     - AttributeError
+
+
+# Split:
+#   output_requirements:
+#     out_file: [in_file, dimension]
+#   output_templates:
+#   doctest:
+#   tests_inputs:
+#     -
+#   tests_outputs:
+#     - AttributeError

example-specs/freesurfer_preprocess_param.yml

@@ -0,0 +1,9 @@
+ApplyVolTransform:
+  output_requirements: []
+  output_templates:
+    transformed_file: "{source_file}_warped"
+  doctest:
+    source_file: test.nii.gz
+    cmdline: mri_vol2vol
+  tests_inputs: []
+  tests_outputs: []

nipype2pydra/cli.py

@@ -13,7 +13,13 @@ def cli():
 
 
 @cli.command(
-    help="Port Nipype task interface code to Pydra"
+    help="""Port Nipype task interface code to Pydra
+
+SPEC_FILE is a YAML file which defines the manually specified aspects of the conversion
+see https://github.com/nipype/nipype2pydra/tree/main/example-specs for examples
+
+OUT_FILE is where the converted code will be generated
+"""
 )
 @click.argument("spec-file", type=click.File())
 @click.argument("out-file", type=click.File(mode="w"))