@@ -39,7 +39,7 @@ above example we have used the ``desc`` metadata which holds human readable
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description of the input. The ``mandatory `` flag forces Nipype to throw an
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exception if the input was not set. ``exists `` is a special flag that works only
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for ``File traits `` and checks if the provided file exists. More details can be
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- found at `interface_specs `_ .
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+ found at :ref: `interface_specs `.
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The input and output specifications have to be connected to the our example
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interface class:
@@ -80,7 +80,7 @@ symbols. For an input defined in InputSpec to be included into the executed
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commandline ``argstr `` has to be included. Additionally inside the main
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interface class you need to specify the name of the executable by assigning it
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to the ``_cmd `` field. Also the main interface class needs to inherit from
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- `CommandLine `_ :
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+ :class: `CommandLine <nipype.interfaces.base.CommandLine> ` :
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.. testcode ::
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@@ -92,7 +92,7 @@ to the ``_cmd`` field. Also the main interface class needs to inherit from
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There is one more thing we need to take care of. When the executable finishes
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processing it will presumably create some output files. We need to know which
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files to look for, check if they exist and expose them to whatever node would
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- like to use them. This is done by implementing `_list_outputs `_ method in the
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+ like to use them. This is done by implementing :func: `_list_outputs <nipype.interfaces.base.BaseInterface._list_outputs> ` method in the
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main interface class. Basically what it does is assigning the expected output
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files to the fields of our output spec:
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