Add individual options as alternative to configuration string (#11)

* Draft CLI reorganization.

* Work on the parser.

* Split up extras and combine with extra_kwargs.

* Split out _get_parser function.

* Update usage.rst

docs/usage.rst

@@ -0,0 +1,90 @@
+#########################################
+Using patch-denoise from the command line
+#########################################
+
+``patch-denoise`` minimally requires a path to a NIfTI file,
+but it can take advantage of reconstructed phase data and/or noise volumes.
+
+.. argparse::
+   :ref: patch_denoise.bindings.cli._get_parser
+   :prog: patch-denoise
+   :func: _get_parser
+
+
+================================
+Using patch-denoise on BIDS data
+================================
+
+.. warning::
+    These examples assume that the phase data are in radians.
+    If they are in arbitrary units,
+    you will need to rescale them before running patch-denoise.
+
+
+Magnitude only
+==============
+
+.. code-block:: bash
+
+    patch-denoise \
+        sub-01/func/sub-01_task-rest_part-mag_bold.nii.gz \
+        sub-01_task-rest_part-mag_desc-denoised_bold.nii.gz \
+        --mask auto \
+        --method optimal-fro \
+        --patch-shape 11 \
+        --patch-overlap 5 \
+        --recombination weighted \
+        --mask-threshold 1
+
+
+Magnitude with noise volumes
+============================
+
+.. code-block:: bash
+
+    patch-denoise \
+        sub-01/func/sub-01_task-rest_part-mag_bold.nii.gz \
+        sub-01_task-rest_part-mag_desc-denoised_bold.nii.gz \
+        --noise-map sub-01/func/sub-01_task-rest_part-mag_noRF.nii.gz \
+        --mask auto \
+        --method optimal-fro \
+        --patch-shape 11 \
+        --patch-overlap 5 \
+        --recombination weighted \
+        --mask-threshold 1
+
+
+Magnitude and phase
+===================
+
+.. code-block:: bash
+
+    patch-denoise \
+        sub-01/func/sub-01_task-rest_part-mag_bold.nii.gz \
+        sub-01_task-rest_part-mag_desc-denoised_bold.nii.gz \
+        --input-phase sub-01/func/sub-01_task-rest_part-phase_bold.nii.gz \
+        --mask auto \
+        --method optimal-fro \
+        --patch-shape 11 \
+        --patch-overlap 5 \
+        --recombination weighted \
+        --mask-threshold 1
+
+
+Magnitude and phase with noise volumes
+======================================
+
+.. code-block:: bash
+
+    patch-denoise \
+        sub-01/func/sub-01_task-rest_part-mag_bold.nii.gz \
+        sub-01_task-rest_part-mag_desc-denoised_bold.nii.gz \
+        --input-phase sub-01/func/sub-01_task-rest_part-phase_bold.nii.gz \
+        --noise-map sub-01/func/sub-01_task-rest_part-mag_noRF.nii.gz \
+        --noise-map-phase sub-01/func/sub-01_task-rest_part-phase_noRF.nii.gz \
+        --mask auto \
+        --method optimal-fro \
+        --patch-shape 11 \
+        --patch-overlap 5 \
+        --recombination weighted \
+        --mask-threshold 1