update make specs

Author: juhuntenburg

nipype/interfaces/afni/tests/test_auto_Volreg.py

@@ -32,6 +32,11 @@ def test_Volreg_inputs():
     name_source='in_file',
     name_template='%s.1D',
     ),
+    oned_matrix_save=dict(argstr='-1Dmatrix_save %s',
+    keep_extension=True,
+    name_source='in_file',
+    name_template='%s.aff12.1D',
+    ),
     out_file=dict(argstr='-prefix %s',
     name_source='in_file',
     name_template='%s_volreg',
@@ -57,6 +62,7 @@ def test_Volreg_inputs():
 def test_Volreg_outputs():
     output_map = dict(md1d_file=dict(),
     oned_file=dict(),
+    oned_matrix_save=dict(),
     out_file=dict(),
     )
     outputs = Volreg.output_spec()

nipype/interfaces/ants/tests/test_auto_N4BiasFieldCorrection.py

@@ -5,6 +5,8 @@
 def test_N4BiasFieldCorrection_inputs():
     input_map = dict(args=dict(argstr='%s',
     ),
+    bias_image=dict(hash_files=False,
+    ),
     bspline_fitting_distance=dict(argstr='--bsline-fitting [%g]',
     ),
     convergence_threshold=dict(argstr=',%g]',
@@ -37,6 +39,10 @@ def test_N4BiasFieldCorrection_inputs():
     genfile=True,
     hash_files=False,
     ),
+    save_bias=dict(mandatory=True,
+    usedefault=True,
+    xor=['bias_image'],
+    ),
     shrink_factor=dict(argstr='--shrink-factor %d',
     ),
     terminal_output=dict(mandatory=True,
@@ -50,7 +56,8 @@ def test_N4BiasFieldCorrection_inputs():
             yield assert_equal, getattr(inputs.traits()[key], metakey), value
 
 def test_N4BiasFieldCorrection_outputs():
-    output_map = dict(output_image=dict(),
+    output_map = dict(bias_image=dict(),
+    output_image=dict(),
     )
     outputs = N4BiasFieldCorrection.output_spec()
 

nipype/interfaces/camino/tests/test_auto_ProcStreamlines.py

@@ -56,14 +56,18 @@ def test_ProcStreamlines_inputs():
     position=-1,
     ),
     outputacm=dict(argstr='-outputacm',
+    requires=['outputroot', 'seedfile'],
     ),
     outputcbs=dict(argstr='-outputcbs',
+    requires=['outputroot', 'targetfile', 'seedfile'],
     ),
     outputcp=dict(argstr='-outputcp',
+    requires=['outputroot', 'seedfile'],
     ),
     outputroot=dict(argstr='-outputroot %s',
     ),
     outputsc=dict(argstr='-outputsc',
+    requires=['outputroot', 'seedfile'],
     ),
     outputtracts=dict(argstr='-outputtracts',
     ),
@@ -103,7 +107,8 @@ def test_ProcStreamlines_inputs():
             yield assert_equal, getattr(inputs.traits()[key], metakey), value
 
 def test_ProcStreamlines_outputs():
-    output_map = dict(proc=dict(),
+    output_map = dict(outputroot_files=dict(),
+    proc=dict(),
     )
     outputs = ProcStreamlines.output_spec()
 

nipype/interfaces/fsl/tests/test_auto_ApplyTOPUP.py

@@ -16,20 +16,28 @@ 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=dict(argstr='--topup=%s',
-    mandatory=True,
+    in_topup_fieldcoef=dict(argstr='--topup=%s',
+    copyfile=False,
+    requires=['in_topup_movpar'],
+    ),
+    in_topup_movpar=dict(copyfile=False,
+    requires=['in_topup_fieldcoef'],
     ),
     interp=dict(argstr='--interp=%s',
     ),
     method=dict(argstr='--method=%s',
     ),
-    out_base=dict(argstr='--out=%s',
+    out_corrected=dict(argstr='--out=%s',
+    name_source=['in_files'],
+    name_template='%s_corrected',
     ),
     output_type=dict(),
     terminal_output=dict(mandatory=True,

nipype/interfaces/fsl/tests/test_auto_DTIFit.py

@@ -17,7 +17,7 @@ def test_DTIFit_inputs():
     mandatory=True,
     position=3,
     ),
-    cni=dict(argstr='-cni %s',
+    cni=dict(argstr='--cni=%s',
     ),
     dwi=dict(argstr='-k %s',
     mandatory=True,

nipype/interfaces/fsl/tests/test_auto_Eddy.py

@@ -33,7 +33,10 @@ def test_Eddy_inputs():
     in_mask=dict(argstr='--mask=%s',
     mandatory=True,
     ),
-    in_topup=dict(argstr='--topup=%s',
+    in_topup_fieldcoef=dict(argstr='--topup=%s',
+    requires=['in_topup_movpar'],
+    ),
+    in_topup_movpar=dict(requires=['in_topup_fieldcoef'],
     ),
     method=dict(argstr='--resamp=%s',
     ),

nipype/interfaces/fsl/tests/test_auto_EddyCorrect.py

@@ -16,14 +16,16 @@ def test_EddyCorrect_inputs():
     position=0,
     ),
     out_file=dict(argstr='%s',
-    genfile=True,
-    hash_files=False,
+    name_source=['in_file'],
+    name_template='%s_edc',
+    output_name='eddy_corrected',
     position=1,
     ),
     output_type=dict(),
     ref_num=dict(argstr='%d',
     mandatory=True,
     position=2,
+    usedefault=True,
     ),
     terminal_output=dict(mandatory=True,
     nohash=True,

nipype/interfaces/fsl/tests/test_auto_FIRST.py

@@ -18,6 +18,7 @@ def test_FIRST_inputs():
     usedefault=True,
     ),
     in_file=dict(argstr='-i %s',
+    copyfile=False,
     mandatory=True,
     position=-2,
     ),

nipype/interfaces/fsl/tests/test_auto_FUGUE.py

@@ -21,7 +21,6 @@ def test_FUGUE_inputs():
     fmap_in_file=dict(argstr='--loadfmap=%s',
     ),
     fmap_out_file=dict(argstr='--savefmap=%s',
-    hash_files=False,
     ),
     forward_warping=dict(usedefault=True,
     ),
@@ -53,21 +52,23 @@ def test_FUGUE_inputs():
     ),
     phase_conjugate=dict(argstr='--phaseconj',
     ),
-    phasemap_file=dict(argstr='--phasemap=%s',
+    phasemap_in_file=dict(argstr='--phasemap=%s',
     ),
     poly_order=dict(argstr='--poly=%d',
     ),
-    save_shift=dict(),
+    save_fmap=dict(xor=['save_unmasked_fmap'],
+    ),
+    save_shift=dict(xor=['save_unmasked_shift'],
+    ),
     save_unmasked_fmap=dict(argstr='--unmaskfmap',
-    requires=['fmap_out_file'],
+    xor=['save_fmap'],
     ),
     save_unmasked_shift=dict(argstr='--unmaskshift',
-    requires=['shift_out_file'],
+    xor=['save_shift'],
     ),
     shift_in_file=dict(argstr='--loadshift=%s',
     ),
     shift_out_file=dict(argstr='--saveshift=%s',
-    hash_files=False,
     ),
     smooth2d=dict(argstr='--smooth2=%.2f',
     ),
@@ -79,11 +80,12 @@ def test_FUGUE_inputs():
     unwarp_direction=dict(argstr='--unwarpdir=%s',
     ),
     unwarped_file=dict(argstr='--unwarp=%s',
-    genfile=True,
-    hash_files=False,
+    requires=['in_file'],
+    xor=['warped_file'],
     ),
     warped_file=dict(argstr='--warp=%s',
-    hash_files=False,
+    requires=['in_file'],
+    xor=['unwarped_file'],
     ),
     )
     inputs = FUGUE.input_spec()

nipype/interfaces/fsl/tests/test_auto_MELODIC.py

@@ -32,6 +32,7 @@ def test_MELODIC_inputs():
     in_files=dict(argstr='-i %s',
     mandatory=True,
     position=0,
+    sep=',',
     ),
     log_power=dict(argstr='--logPower',
     ),