fix: arg generation

Author: satra

nipype/interfaces/fsl/epi.py

@@ -264,11 +264,11 @@ def _overload_extension(self, value, name=None):
 class ApplyTOPUPInputSpec(FSLCommandInputSpec):
     in_files = InputMultiPath(File(exists=True), mandatory=True,
                               desc='name of 4D file with images',
-                              argstr='--imain=%s...', sep=',')
+                              argstr='--imain=%s', sep=',')
     encoding_file = File(exists=True, mandatory=True,
                          desc='name of text file with PE directions/times',
                          argstr='--datain=%s')
-    in_index = traits.List(traits.Int, argstr='--inindex=%d...', sep=',',
+    in_index = traits.List(traits.Int, argstr='--inindex=%s', sep=',',
                            mandatory=True,
                            desc=('comma separated list of indicies into '
                                  '--datain of the input image (to be '
@@ -313,7 +313,7 @@ class ApplyTOPUP( FSLCommand ):
         >>> applytopup.inputs.in_topup_fieldcoef = "topup_fieldcoef.nii.gz"
         >>> applytopup.inputs.in_topup_movpar = "topup_movpar.txt"
         >>> applytopup.cmdline #doctest: +ELLIPSIS
-        'applytopup --datain=topup_encoding.txt --imain=epi.nii,--imain=epi_rev.nii --inindex=1,--inindex=2 --topup=topup --out=epi_corrected.nii.gz'
+        'applytopup --datain=topup_encoding.txt --imain=epi.nii,epi_rev.nii --inindex=1,2 --topup=topup --out=epi_corrected.nii.gz'
         >>> res = applytopup.run() # doctest: +SKIP
 
     """

nipype/interfaces/fsl/tests/test_auto_ApplyTOPUP.py

@@ -16,11 +16,13 @@ def test_ApplyTOPUP_inputs():
     ignore_exception=dict(nohash=True,
     usedefault=True,
     ),
-    in_files=dict(argstr='%s',
+    in_files=dict(argstr='--imain=%s',
     mandatory=True,
+    sep=',',
     ),
-    in_index=dict(argstr='%s',
+    in_index=dict(argstr='--inindex=%s',
     mandatory=True,
+    sep=',',
     ),
     in_topup_fieldcoef=dict(argstr='--topup=%s',
     copyfile=False,