changes dwifslpreproc outputs' configuration and reset tests to match the new one

Author: GalKepler

nipype/interfaces/mrtrix3/preprocess.py

@@ -192,7 +192,9 @@ class DWIBiasCorrectInputSpec(MRTrix3BaseInputSpec):
         mandatory=True,
         desc="input DWI image",
     )
-    in_mask = File(argstr="-mask %s", desc="input mask image for bias field estimation")
+    in_mask = File(
+        argstr="-mask %s", desc="input mask image for bias field estimation"
+    )
     use_ants = traits.Bool(
         argstr="ants",
         mandatory=True,
@@ -333,25 +335,16 @@ class DWIPreprocInputSpec(MRTrix3BaseInputSpec):
         argstr="-eddyqc_all %s",
         desc="Copy ALL outputs generated by eddy (including images), and the output of eddy_qc (if installed), into an output directory",
     )
-    export_grad_mrtrix = traits.Bool(
-        argstr="-export_grad_mrtrix",
-        desc="export new gradient files in mrtrix format",
-    )
-    export_grad_fsl = traits.Bool(
-        argstr="-export_grad_fsl", desc="export gradient files in FSL format"
-    )
     out_grad_mrtrix = File(
         "grad.b",
-        argstr="%s",
-        requires=["export_grad_mrtrix"],
-        desc="name of new gradient file",
+        argstr="-export_grad_mrtrix %s",
+        desc="export new gradient files in mrtrix format",
     )
     out_grad_fsl = traits.Tuple(
         File("grad.bvecs", desc="bvecs"),
         File("grad.bvals", desc="bvals"),
-        argstr="%s, %s",
-        requires=["export_grad_fsl"],
-        desc="Output (bvecs, bvals) gradients FSL format",
+        argstr="-export_grad_fsl %s, %s",
+        desc="export gradient files in FSL format",
     )
 
 
@@ -409,7 +402,9 @@ def _list_outputs(self):
         outputs = self.output_spec().get()
         outputs["out_file"] = op.abspath(self.inputs.out_file)
         if self.inputs.export_grad_mrtrix:
-            outputs["out_grad_mrtrix"] = op.abspath(self.inputs.out_grad_mrtrix)
+            outputs["out_grad_mrtrix"] = op.abspath(
+                self.inputs.out_grad_mrtrix
+            )
         if self.inputs.export_grad_fsl:
             outputs["out_fsl_bvec"] = op.abspath(self.inputs.out_grad_fsl[0])
             outputs["out_fsl_bval"] = op.abspath(self.inputs.out_grad_fsl[1])
@@ -443,9 +438,15 @@ class ResponseSDInputSpec(MRTrix3BaseInputSpec):
         usedefault=True,
         desc="output WM response text file",
     )
-    gm_file = File(argstr="%s", position=-2, desc="output GM response text file")
-    csf_file = File(argstr="%s", position=-1, desc="output CSF response text file")
-    in_mask = File(exists=True, argstr="-mask %s", desc="provide initial mask image")
+    gm_file = File(
+        argstr="%s", position=-2, desc="output GM response text file"
+    )
+    csf_file = File(
+        argstr="%s", position=-1, desc="output CSF response text file"
+    )
+    in_mask = File(
+        exists=True, argstr="-mask %s", desc="provide initial mask image"
+    )
     max_sh = InputMultiObject(
         traits.Int,
         argstr="-lmax %s",

nipype/interfaces/mrtrix3/tests/test_auto_DWIPreproc.py

@@ -34,12 +34,6 @@ def test_DWIPreproc_inputs():
             nohash=True,
             usedefault=True,
         ),
-        export_grad_fsl=dict(
-            argstr="-export_grad_fsl",
-        ),
-        export_grad_mrtrix=dict(
-            argstr="-export_grad_mrtrix",
-        ),
         grad_file=dict(
             argstr="-grad %s",
             extensions=None,
@@ -89,13 +83,11 @@ def test_DWIPreproc_inputs():
             usedefault=True,
         ),
         out_grad_fsl=dict(
-            argstr="%s, %s",
-            requires=["export_grad_fsl"],
+            argstr="-export_grad_fsl %s, %s",
         ),
         out_grad_mrtrix=dict(
-            argstr="%s",
+            argstr="-export_grad_mrtrix %s",
             extensions=None,
-            requires=["export_grad_mrtrix"],
         ),
         pe_dir=dict(
             argstr="-pe_dir %s",