fix automatic name forward of name_template

Author: oesteban

nipype/interfaces/afni/preprocess.py

@@ -2392,8 +2392,9 @@ class OutlierCountInputSpec(CommandLineInputSpec):
                            desc='write out the median + 3.5 MAD of outlier'
                                 ' count with each timepoint')
     save_outliers = traits.Bool(False, usedefault=True, desc='enables out_file option')
-    outliers_file = File(name_template="%s_outliers", argstr='-save %s', name_source=["in_file"],
-                         keep_extension=True, desc='output image file name')
+    outliers_file = File(
+        name_template="%s_outliers", argstr='-save %s', name_source=["in_file"],
+        output_name='out_outliers', keep_extension=True, desc='output image file name')
 
     polort = traits.Int(argstr='-polort %d',
                         desc='detrend each voxel timeseries with polynomials')
@@ -2405,7 +2406,7 @@ class OutlierCountInputSpec(CommandLineInputSpec):
 
 
 class OutlierCountOutputSpec(TraitedSpec):
-    outliers_file = File(exists=True, desc='output image file name')
+    out_outliers = File(exists=True, desc='output image file name')
     out_file = File(
         name_template='%s_tqual', name_source=['in_file'], argstr='> %s',
         keep_extension=False, position=-1, desc='capture standard output')
@@ -2441,6 +2442,11 @@ def _parse_inputs(self, skip=None):
             skip += ['outliers_file']
         return super(OutlierCount, self)._parse_inputs(skip)
 
+    def _list_outputs(self):
+        outputs = self.output_spec().get()
+        if self.inputs.save_outliers:
+            outputs['out_outliers'] = op.abspath(self.inputs.outliers_file)
+
 
 class QualityIndexInputSpec(CommandLineInputSpec):
     in_file = File(argstr='%s', mandatory=True, exists=True, position=-2, desc='input dataset')

nipype/interfaces/afni/tests/test_auto_OutlierCount.py

@@ -46,6 +46,7 @@ def test_OutlierCount_inputs():
     keep_extension=True,
     name_source=['in_file'],
     name_template='%s_outliers',
+    output_name='out_outliers',
     ),
     polort=dict(argstr='-polort %d',
     ),
@@ -70,7 +71,7 @@ def test_OutlierCount_outputs():
     name_template='%s_tqual',
     position=-1,
     ),
-    outliers_file=dict(),
+    out_outliers=dict(),
     )
     outputs = OutlierCount.output_spec()
 

nipype/interfaces/freesurfer/tests/test_auto_MRIsConvert.py

@@ -30,10 +30,12 @@ def test_MRIsConvert_inputs():
     ),
     origname=dict(argstr='-o %s',
     ),
-    out_datatype=dict(xor=['out_file'],
+    out_datatype=dict(mandatory=True,
+    xor=['out_file'],
     ),
     out_file=dict(argstr='%s',
     genfile=True,
+    mandatory=True,
     position=-1,
     xor=['out_datatype'],
     ),

nipype/interfaces/freesurfer/utils.py

@@ -852,7 +852,7 @@ def _format_arg(self, name, spec, value):
         if name == "out_file" and not os.path.isabs(value):
             value = os.path.abspath(value)
         return super(MRIsConvert, self)._format_arg(name, spec, value)
-    
+
     def _list_outputs(self):
         outputs = self.output_spec().get()
         outputs["converted"] = os.path.abspath(self._gen_outfilename())