> So is the behavior of the optional="true" tag that if the field form is left
> empty for that parameter then it will not be passed to the tool?
Optional is enforced at the UI level; a wrapper can choose to handle optional
parameters differently.
> I am wondering if a more sophisticated behavi
Thanks for the pointer to the updated wrapper and the optional tag.
So is the behavior of the optional="true" tag that if the field form is
left empty for that parameter then it will not be passed to the tool?
I am wondering if a more sophisticated behavior on the UI side of things
for the "option
>
> Wouldn't it be better not to have the default value 40 (or 20) in the wrapper
> at all? i.e. Leave it out, so that by default that argument isn't used, so
> that
> tophat uses the default it wants to use.
This would work but limits reproducibility and transparency because Galaxy
wouldn't ha
On Fri, Feb 10, 2012 at 4:18 PM, Jeremy Goecks wrote:
>> On Thu, Feb 9, 2012 at 11:27 PM, Andrew Warren wrote:
>>> Hello,
>>>
>>> I was recently adjusting advanced parameters when running Tophat in Galaxy
>>> and noticed that when advanced parameters are used, every field is converted
>>> and sub
> On Thu, Feb 9, 2012 at 11:27 PM, Andrew Warren wrote:
>> Hello,
>>
>> I was recently adjusting advanced parameters when running Tophat in Galaxy
>> and noticed that when advanced parameters are used, every field is converted
>> and submitted as command line parameter to the tool at runtime. Wit
On Thu, Feb 9, 2012 at 11:27 PM, Andrew Warren wrote:
> Hello,
>
> I was recently adjusting advanced parameters when running Tophat in Galaxy
> and noticed that when advanced parameters are used, every field is converted
> and submitted as command line parameter to the tool at runtime. Without
> c
Hello,
I was recently adjusting advanced parameters when running Tophat in Galaxy
and noticed that when advanced parameters are used, every field is
converted and submitted as command line parameter to the tool at runtime.
Without changing any of the default values I get a different tophat result
