diff --git a/nipype/interfaces/afni/preprocess.py b/nipype/interfaces/afni/preprocess.py
index 13a065c27c..9ede8d13e0 100644
--- a/nipype/interfaces/afni/preprocess.py
+++ b/nipype/interfaces/afni/preprocess.py
@@ -218,7 +218,9 @@ class AllineateInputSpec(AFNICommandInputSpec):
     out_file = File(
         desc='output file from 3dAllineate',
         argstr='-prefix %s',
-        genfile=True,
+        name_template='%s_allineate',
+        name_source='in_file',
+        hash_files=False,
         xor=['allcostx'])
     out_param_file = File(
         argstr='-1Dparam_save %s',
@@ -424,11 +426,11 @@ class AllineateInputSpec(AFNICommandInputSpec):
     _dirs = ['X', 'Y', 'Z', 'I', 'J', 'K']
     nwarp_fixmot = traits.List(
         traits.Enum(*_dirs),
-        argstr='-nwarp_fixmot%s',
+        argstr='-nwarp_fixmot%s...',
         desc='To fix motion along directions.')
     nwarp_fixdep = traits.List(
         traits.Enum(*_dirs),
-        argstr='-nwarp_fixdep%s',
+        argstr='-nwarp_fixdep%s...',
         desc='To fix non-linear warp dependency along directions.')
     verbose = traits.Bool(
         argstr='-verb', desc='Print out verbose progress reports.')
@@ -465,7 +467,6 @@ class Allineate(AFNICommand):
     '3dAllineate -source functional.nii -prefix functional_allineate.nii -1Dmatrix_apply cmatrix.mat'
     >>> res = allineate.run()  # doctest: +SKIP
 
-    >>> from nipype.interfaces import afni
     >>> allineate = afni.Allineate()
     >>> allineate.inputs.in_file = 'functional.nii'
     >>> allineate.inputs.reference = 'structural.nii'
@@ -473,23 +474,22 @@ class Allineate(AFNICommand):
     >>> allineate.cmdline
     '3dAllineate -source functional.nii -base structural.nii -allcostx |& tee out.allcostX.txt'
     >>> res = allineate.run()  # doctest: +SKIP
+
+    >>> allineate = afni.Allineate()
+    >>> allineate.inputs.in_file = 'functional.nii'
+    >>> allineate.inputs.reference = 'structural.nii'
+    >>> allineate.inputs.nwarp_fixmot = ['X', 'Y']
+    >>> allineate.cmdline
+    '3dAllineate -source functional.nii -nwarp_fixmotX -nwarp_fixmotY -prefix functional_allineate -base structural.nii'
+    >>> res = allineate.run()  # doctest: +SKIP
     """
 
     _cmd = '3dAllineate'
     input_spec = AllineateInputSpec
     output_spec = AllineateOutputSpec
 
-    def _format_arg(self, name, trait_spec, value):
-        if name == 'nwarp_fixmot' or name == 'nwarp_fixdep':
-            arg = ' '.join([trait_spec.argstr % v for v in value])
-            return arg
-        return super(Allineate, self)._format_arg(name, trait_spec, value)
-
     def _list_outputs(self):
-        outputs = self.output_spec().get()
-
-        if self.inputs.out_file:
-            outputs['out_file'] = op.abspath(self.inputs.out_file)
+        outputs = super(Allineate, self)._list_outputs()
 
         if self.inputs.out_weight_file:
             outputs['out_weight_file'] = op.abspath(
@@ -512,16 +512,10 @@ def _list_outputs(self):
                 outputs['out_param_file'] = op.abspath(
                     self.inputs.out_param_file)
 
-        if isdefined(self.inputs.allcostx):
-            outputs['allcostX'] = os.path.abspath(
-                os.path.join(os.getcwd(), self.inputs.allcostx))
+        if self.inputs.allcostx:
+            outputs['allcostX'] = os.path.abspath(self.inputs.allcostx)
         return outputs
 
-    def _gen_filename(self, name):
-        if name == 'out_file':
-            return self._list_outputs()[name]
-        return None
-
 
 class AutoTcorrelateInputSpec(AFNICommandInputSpec):
     in_file = File(
diff --git a/nipype/interfaces/afni/tests/test_auto_Allineate.py b/nipype/interfaces/afni/tests/test_auto_Allineate.py
index 59b1929fbe..1c5476a429 100644
--- a/nipype/interfaces/afni/tests/test_auto_Allineate.py
+++ b/nipype/interfaces/afni/tests/test_auto_Allineate.py
@@ -61,12 +61,14 @@ def test_Allineate_inputs():
             usedefault=True,
         ),
         nwarp=dict(argstr='-nwarp %s', ),
-        nwarp_fixdep=dict(argstr='-nwarp_fixdep%s', ),
-        nwarp_fixmot=dict(argstr='-nwarp_fixmot%s', ),
+        nwarp_fixdep=dict(argstr='-nwarp_fixdep%s...', ),
+        nwarp_fixmot=dict(argstr='-nwarp_fixmot%s...', ),
         one_pass=dict(argstr='-onepass', ),
         out_file=dict(
             argstr='-prefix %s',
-            genfile=True,
+            hash_files=False,
+            name_source='in_file',
+            name_template='%s_allineate',
             xor=['allcostx'],
         ),
         out_matrix=dict(
diff --git a/nipype/interfaces/base/core.py b/nipype/interfaces/base/core.py
index c199af3ca8..d15628fd6b 100644
--- a/nipype/interfaces/base/core.py
+++ b/nipype/interfaces/base/core.py
@@ -1072,6 +1072,12 @@ def _filename_from_source(self, name, chain=None):
         if not isdefined(retval) or "%s" in retval:
             if not trait_spec.name_source:
                 return retval
+
+            # Do not generate filename when excluded by other inputs
+            if trait_spec.xor and any(isdefined(getattr(self.inputs, field))
+                                      for field in trait_spec.xor):
+                return retval
+
             if isdefined(retval) and "%s" in retval:
                 name_template = retval
             else: