Re: [galaxy-dev] Setting the output label based on input parameters?

2012-02-27 Thread Ann Black-Ziegelbein
We are also feeling the hurt of not being able to carry the input dataset names through a complex workflow. We are also very interested in a solution similar to what Dave Walton has proposed,. Dave, would it be possible to receive a copy of your modified code? Does it work when there are

Re: [galaxy-dev] Setting the output label based on input parameters?

2011-09-15 Thread Ross
on_string seems to be defined for datatool parameters only. There's a common idiom for looking up fields from the relevant .loc files for things like all_fasta - it's not pretty but it does work - eg from the bowtie wrapper: --ref=${ filter( lambda x: str( x[0] ) == str( $refGenomeSource.index

Re: [galaxy-dev] Setting the output label based on input parameters?

2011-09-01 Thread Dave Walton
This is similar to something we've done for workflows in our instance of Galaxy. Dannon actually suggested I push a copy of my changes out so he can review them and potentially add them to galaxy central. I've been delinquent in doing this push. It's not exactly what you are talking about but

Re: [galaxy-dev] Setting the output label based on input parameters?

2011-09-01 Thread Dave Walton
This is a big part of the reason we did this. I will push it out for the galaxy team to look at. If for some reason the don't approve it I can share our change directly with you. Dave On Sep 1, 2011, at 6:39 PM, Ross ross.laza...@gmail.com wrote: FWIW: This sounds like a useful idea to me.

Re: [galaxy-dev] Setting the output label based on input parameters?

2011-08-29 Thread Nikhil Joshi
It looks like the Cheetah syntax only is parsed within the command tags so I figured out a way to do it... but it seems hackish. I basically changed the string values of truevalue and falsevalue within the parameter to be an English sentence that would become the label for the output. I.e.,

Re: [galaxy-dev] Setting the output label based on input parameters?

2011-08-29 Thread Ross
On Thu, Aug 25, 2011 at 6:34 AM, SHAUN WEBB swe...@staffmail.ed.ac.uk wrote: I meant to say label=${input} or label=${input.value}. Nikhil, did you try as Shaun and others have suggested? Any available string parameter can be used in a label as far as I can tell. This is a common idiom -

Re: [galaxy-dev] Setting the output label based on input parameters?

2011-08-29 Thread Nikhil Joshi
Hi Ross, Yes, I did try that... but what I want is string parameter that changes based on whether or not you've checked a checkbox (or a way to change the label of the output based on whether or not the checkbox was checked). So my idea below did work, but it seems like a hack. Which is why I

Re: [galaxy-dev] Setting the output label based on input parameters?

2011-08-29 Thread Ross
Most times I need a user supplied label substring. I'm not sure how else to conditionally set a string to a predetermined value other than with boolean true/false strings or select parameter values. One even more ugly option is to use a (strictly speaking now deprecated) post job exec hook to

Re: [galaxy-dev] Setting the output label based on input parameters?

2011-08-25 Thread Nikhil Joshi
Hi Kanwei, I tried that and it didn't seem to work. It seems like Galaxy parses the output name BEFORE execution... although that doesn't make sense. In any case, I couldn't get it to work. Also, in the example below the % should really be # right? Anything anyone can think of that I might be

Re: [galaxy-dev] Setting the output label based on input parameters?

2011-08-25 Thread SHAUN WEBB
you can use label=${input.name} Shaun Quoting Nikhil Joshi najo...@ucdavis.edu on Thu, 25 Aug 2011 03:10:21 -0700: Hi Kanwei, I tried that and it didn't seem to work. It seems like Galaxy parses the output name BEFORE execution... although that doesn't make sense. In any case, I

Re: [galaxy-dev] Setting the output label based on input parameters?

2011-08-25 Thread Nikhil Joshi
It's actually a boolean checkbox. so I basically want the label to change based upon whether or not the checkbox is checked. Is there any way to do that? Again, I've tried using the Cheetah syntax to do the #if #end inside the output tags but that didn't work. - Nik. On Thu, Aug 25,

Re: [galaxy-dev] Setting the output label based on input parameters?

2011-08-24 Thread Kanwei Li
Hi Nikhil, The tool templates are Cheetah templates, so you can do things like: outputs %if param == True: data format=txt name=blah label=Label1 / %else data format=txt name=blah label=Label2 / %endif /outputs Thanks, K On Wed, Aug 24, 2011 at 8:24 PM, Nikhil Joshi najo...@ucdavis.edu