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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