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 "optional" tag would still allow for recording that the parameter is using the default value for the version of that tool but not actually pass that parameter on the command line in case it influences the behavior of the tool? Thinking of parameters that should have a default value but whose actual presence on the command line changes what happens. Though, I guess this could be done by simply deleting the default value in the optional parameter has one? Maybe if the optional tag enabled the parameter itself to be toggled on/off (grayed out/regular text)? This way a block of advanced parameters could be enabled without requiring that they all be passed to the tool (or deleting all their values if they are marked optional). Just a small note, the update to the tophat wrapper was to the maximum number of alignments instead of mismatches. Thanks again, Andrew On Fri, Feb 10, 2012 at 11:28 AM, Peter Cock <p.j.a.cock@googlemail.com>wrote:
On Thu, Feb 9, 2012 at 11:27 PM, Andrew Warren <anwarren@vbi.vt.edu> 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 changing any of the default values I get a different tophat result
On Fri, Feb 10, 2012 at 4:18 PM, Jeremy Goecks <jeremy.goecks@emory.edu> wrote: than if
advanced parameters are left off.
That sounds like a bug in the wrapper.
Recent Tophat versions have changed parameters and default values again. I made the following changes in 3bd8bed55631 to make the wrapper compatible with Tophat 1.4.0:
*removed junctions_filter parameter *changed the default value for max-mismatches from 40 to 20
This should ensure that enabling advanced parameters but leaving them untouched yields the same results as using default parameters.
J.
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.
Peter