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.
> 
> My users are struggling with output names currently being generated by
> complex workflows where many tools do something like
> label="${tool.name} on ${on_string}: reordered ${outputFormat}" - that
> might be ok for a single step but after traveling through a few of
> those, the base name (which we routinely use for metadata needed at
> some final amalgamation step, such as experimental condition) is hard
> to find in all the cruft.
> 
> 
> 
> On Thu, Sep 1, 2011 at 11:16 PM, Dave Walton <dave.wal...@jax.org> wrote:
>> 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 similar (IMHO)...  If folks are interested in this functionality I'll
>> get off my butt and make the time to share the changes.
>> 
>> In brief, here's what I did:
>> 
>> The change is totally isolated to lib/galaxy/jobs/actions/post.py in the
>> RenameDatasetAction.execute method.
>> 
>> I have introduced syntax similar to the ${variable} syntax that is used for
>> creating workflow variables.
>> 
>> In my case the syntax is as follows:
>> #{inputs_file_variable | option 1 | option n}
>> where:
>>     input_file_variable = is the name of a module input variable
>>     |  = the delimiter for added options. Optional if no options.
>>     options = basename, upper, lower
>>     basename = keep all of the file name except the extension
>>                (everything before the final ".")
>>     upper = force the file name to upper case
>>     lower = force the file name to lower case
>>  suggested additions:
>>     "replace" option so you can replace a portion of the name,
>>     support multiple #{name} in one rename action...
>> 
>> The choice of the character "#" instead of "$" was relatively arbitrary...
>> It was that or "!" actually.
>> 
>> So an example might be:
>> I have a workflow with an Input Dataset and a FASTQ Groomer.
>> In the FASTQ Groomer I select "Rename Dataset" "output_file" and then in the
>> "New output name:" field I might type:
>> #{input_file | basename | upper}.fastqsanger
>> 
>> Assume the original input file name to the Input Dataset was
>> s_1_1_PWDxNOD.txt
>> The variable in the FastQ Groomer module for that file is "input_file".
>> When I run the workflow, the resulting output file from the groomer would be
>> "S_1_1_PWDXNOD.fastqsanger"
>> 
>> A much simpler example might just be "#{input_file}.fastqsanger".  This is
>> perfectly legal syntax, but the downside is if you have a lengthy workflow
>> and you are continually appending new extentions, you could end up with
>> something like "s_1_1_PWDxNOD.fastqsanger.bam.gex.tab".
>> 
>> Like the first of the two suggested additions I mention above, I could see
>> you deciding to add more possible operations in addition to basename, upper,
>> lower and replace.
>> 
>> The concept of the markup I used for adding the operations was taken from
>> "Liquid markup" (https://github.com/tobi/liquid/wiki/liquid-for-designers).
>> 
>> I welcome any feedback and am more than happy to share the code back to the
>> galaxy community.
>> 
>> Dave
>> 
>> On 8/29/11 6:20 PM, "Ross" <ross.laza...@gmail.com> wrote:
>> 
>>> 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 change the output dataset name based
>>> on some logic - but if the boolean works, I'd recommend moving on :)
>>> 
>>> On Tue, Aug 30, 2011 at 7:56 AM, Nikhil Joshi <najo...@ucdavis.edu> wrote:
>>>> 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 was
>>>> wondering if there was a better way.
>>>> 
>>>> - Nik.
>>>> 
>>>> On Mon, Aug 29, 2011 at 2:55 AM, Ross <ross.laza...@gmail.com> wrote:
>>>>> 
>>>>>>> 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 - ask for a string ('title') to describe the
>>>>> job/output for posterity, then in an output:
>>>>> 
>>>>> <data format="foo" name="output1" metadata_source="input1"
>>>>> label="${title}.myext"/>
>>>>> 
>>>>> There's even a built in ${on_string} if you just want the file name
>>>>> plus some history ids?
>>>>> 
>>>>> 
>>>>> On Mon, Aug 29, 2011 at 6:54 PM, Nikhil Joshi <najo...@ucdavis.edu> wrote:
>>>>>> It looks like the Cheetah syntax only is parsed within the <command>
>>>>>> tags.... so I figured out a way to do it... but it seems hackish.  I
>>>>>> basically changed the string values of truevalue and falsevalue within
>>>>>> the
>>>>>> parameter to be an English sentence that would become the label for the
>>>>>> output.  I.e., in the input section:
>>>>>> 
>>>>>> <param name="filter_reads" type="boolean" truevalue="Filtered Reads
>>>>>> Fasta"
>>>>>> falsevalue="Unfiltered Reads Fasta" label="Filter reads?"/>
>>>>>> 
>>>>>> and in the output section:
>>>>>> 
>>>>>> <data format="fasta" name="output_fasta" label="$filter_reads"/>
>>>>>> 
>>>>>> This seems wrong to do, but it does work.  If anyone has a better
>>>>>> method,
>>>>>> please let me know!
>>>>>> 
>>>>>> - Nik.
>>>>>> 
>>>>>> On Thu, Aug 25, 2011 at 2:36 PM, Nikhil Joshi <najo...@ucdavis.edu>
>>>>>> wrote:
>>>>>>> 
>>>>>>> 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, 2011 at 6:34 AM, SHAUN WEBB <swe...@staffmail.ed.ac.uk>
>>>>>>> wrote:
>>>>>>>> 
>>>>>>>> I meant to say label="${input}" or label="${input.value}.
>>>>>>>> 
>>>>>>>> If it's a select field then you can change the option values to the
>>>>>>>> text
>>>>>>>> you want to add to your output label.
>>>>>>>> 
>>>>>>>> Shaun
>>>>>>>> 
>>>>>>>> 
>>>>>>>> 
>>>>>>>> 
>>>>>>>> 
>>>>>>>> Quoting Kanwei Li <kan...@gmail.com> on Wed, 24 Aug 2011 20:34:57
>>>>>>>> -0400:
>>>>>>>> 
>>>>>>>>> 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>
>>>>>>>>> wrote:
>>>>>>>>> 
>>>>>>>>>> Hi all,
>>>>>>>>>> 
>>>>>>>>>> Is there a way to set the label of the output based on the input
>>>>>>>>>> parameters?  Perhaps by using the <action> tag?  Basically, I want
>>>>>>>>>> the
>>>>>>>>>> output label to be different if the user sets a particular parameter
>>>>>>>>>> to
>>>>>>>>>> be
>>>>>>>>>> true.

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