>> Unfortunately, I can't help much with refresh_on_change either, we just
>> use the <conditional>/<when> tag set. I have been under the impression
>> the the documentation has been written for 'refresh_on_change' in the
>> meantime. I am sorry, I should have checked first, before suggesting it.
> 
> No problem. I’ll know to keep en eye for documentation on this feature :)

refresh_on_change is not a feature that is exposed to tool developers for use 
in tool wrappers. Instead, it's used behind the scenes to make conditional/when 
and dynamic options tags work.

>> Regarding the command line: you can have different commandlines, eg
>> 
>>   <command>
>>     #if   ($summary.mode=="a")#commandline1
>>     #elif ($summary.mode=="b")#commandline2
>>     #elif ($summary.mode=="c")#commandline3
>>     #end if
>>   </command>
>> 
>> and one of those 'commandlines' could be two commands (ie indexing
>> first, followed by the next binary)
> 
> I had not thought of that! That makes sense, yes. I’ll do that.


Frequently, if/else is used to progressively build a command line:

--
my_script.py

#if option1:
        --enable-option1 --option1-parameter $option1-parameter
#elif option2:
        --enable-option1 --option1-parameter $option1-parameter
#endif
--


Best,
J.


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