Overuse of checks for variable presence on required, positional arguments.

[hexylena]

I think some exceptions need to be made for positional arguments to treat them differently, as they're a hard requirement.

e.g.

  <command interpreter="python"><![CDATA[phantasm_data_comparison.py 
#if $positional_1 and $positional_1 is not None:
$positional_1
#end if

#if $positional_2 and $positional_2 is not None:
$positional_2
#end if

#if $positional_3 and $positional_3 is not None:
$positional_3
#end if

#if $positional_4 and $positional_4 is not None:
$positional_4
#end if
> $default]]></command>
  <inputs>
    <param label="First Tabular Dataset (positional_1)" name="positional_1" type="data"/>
    <param label="Second Tabular Dataset (positional_2)" name="positional_2" type="data"/>
    <param label="Method for comparison (positional_3)" name="positional_3">