Merge pull request #1133 from nipy/master

Update to master

Author: blakedewey

CHANGES

@@ -56,6 +56,7 @@ Next release
 * FIX: Add QA output for TSNR to resting workflow (https://github.com/nipy/nipype/pull/1088)
 * FIX: Change N4BiasFieldCorrection to use short tag for dimensionality (backward compatible) (https://github.com/nipy/nipype/pull/1096)
 * ENH: Added -newgrid input to Warp in AFNI (3dWarp wrapper) (https://github.com/nipy/nipype/pull/1128)
+* FIX: Fixed AFNI Copy interface to use positional inputs as required (https://github.com/nipy/nipype/pull/1131)
 
 Release 0.10.0 (October 10, 2014)
 ============

nipype/interfaces/afni/preprocess.py

@@ -676,7 +676,7 @@ class CopyInputSpec(AFNICommandInputSpec):
                    exists=True,
                    copyfile=False)
     out_file = File(name_template="%s_copy", desc='output image file name',
-                    argstr='-prefix %s', name_source="in_file")
+                    argstr='%s', position=-1, name_source="in_file")
 
 
 class Copy(AFNICommand):
@@ -690,11 +690,26 @@ class Copy(AFNICommand):
     ========
 
     >>> from nipype.interfaces import afni as afni
-    >>> copy = afni.Copy()
-    >>> copy.inputs.in_file = 'functional.nii'
-    >>> copy.inputs.out_file = 'new_func.nii'
-    >>> res = copy.run() # doctest: +SKIP
-
+    >>> copy3d = afni.Copy()
+    >>> copy3d.inputs.in_file = 'functional.nii'
+    >>> copy3d.cmdline
+    '3dcopy functional.nii functional_copy'
+
+    >>> from copy import deepcopy
+    >>> copy3d_2 = deepcopy(copy3d)
+    >>> copy3d_2.inputs.outputtype = 'NIFTI'
+    >>> copy3d_2.cmdline
+    '3dcopy functional.nii functional_copy.nii'
+
+    >>> copy3d_3 = deepcopy(copy3d)
+    >>> copy3d_3.inputs.outputtype = 'NIFTI_GZ'
+    >>> copy3d_3.cmdline
+    '3dcopy functional.nii functional_copy.nii.gz'
+
+    >>> copy3d_4 = deepcopy(copy3d)
+    >>> copy3d_4.inputs.out_file = 'new_func.nii'
+    >>> copy3d_4.cmdline
+    '3dcopy functional.nii new_func.nii'
     """
 
     _cmd = '3dcopy'

nipype/interfaces/afni/tests/test_auto_Copy.py

@@ -16,9 +16,10 @@ def test_Copy_inputs():
     mandatory=True,
     position=-2,
     ),
-    out_file=dict(argstr='-prefix %s',
+    out_file=dict(argstr='%s',
     name_source='in_file',
     name_template='%s_copy',
+    position=-1,
     ),
     outputtype=dict(),
     terminal_output=dict(nohash=True,