Input naming deficiencies

[hexylena]

I have a workflow with some N steps, the final file I wish to name based on the filename in the input file. E.g if my input file is "protein A", I wish the final output to be "Your results on protein A".

The problem is that there are the N-2 steps in between start and finish. I have to carry this name along throughout the entire analysis chain, overwriting otherwise useful names on hidden datasets that the user occasionally unhides to look at.

I propose that the rename dataset action support usage of all the dataset names from Input Dataset elements, rather than just input files to the particular tool.

The table shows the current vs optimal scenarios:

Step	Current Syntax	Current Filename	Proposed Syntax	Expected Filename using inputs
Input		A		A
Select Lines	Select Lines on #{input}	Select lines on A	Select lines on #{__input_dataset_1}	Select lines on A
Blast	Blast on #{input}	Blast on Select lines on A	Blast on #{__input_dataset_1}	Blast on A

[remimarenco]

+1 on this, that would be very useful

[dannon]

Deficiency seems like a fairly harsh characterization since you can use workflow parameters to do a very similar thing to this now. Blast on ${primary_sample_dataset}

That said, making formalized workflow inputs available for parameters is probably a nice improvement (though we have to improve the display of 'available variables' significantly since it's already basically limited to expert users).

[hexylena]

Deficiency is just a lack of something, there are no emotions in my words, I assure you. But perhaps that was the wrong word choice for a feature request. It feels like an obvious, missing feature for anyone who uses the rename dataset on larger workflows that biologists use.

${primary_sample_dataset}? That precise term is not documented anywhere so I assume you are using that to mean an input dataset name to a single tool, and just doing what I do, #{input_dataset} for every single tool to pass a filename along to the end of a long analysis chain. Or did I misunderstand?

Anyway with the current "pass this parameter along to the end" I dislike how this affects my history. I have to do this so my end users understand when they get two files at the end, what those files are.

[gregvonkuster]

+1 on this - this would be very useful

[sszakony]

Is it potentially possible that someone would want the input value of an intermediate step at the end, rather than the primary step? I'm not sure how this is structured under the covers of Galaxy, but perhaps it would be more flexible to have an input something like {input, step number}. That way, you'd have a ton of flexibility for saying something like "Blast of A, after filtering via process X". Just a thought.

[lparsons]

I think that issue #2006 would probably fix this. The problem with using workflow variables is that does not allow use on a collection, which is the only feasible solution for working with many samples (most, if not all, of our workflows).

[lparsons]

Naming of files is probably the single biggest issue holding back further usage of Galaxy for us. Here is an attempt to collect various related issues. Perhaps someone on the Galaxy team would like to create one large ticket to collect dataset naming issues (and add to the roadmap #1928?) @jmchilton, @martenson?

Enhancements:

1. Ability to name datasets using the element identifier: Expose element_identifier as a workflow parameter variable. #2006
2. Ability to define the collection name in a workflow: Enhancement: Ability to name collection in a workflow #2398
3. Name datasets according to both collection name and element identifier: Feature request - Filenames based on dataset collection identifier #2140, Download files in a list of datasets with the name from the list #2023

Bug Fixes:

1. Renaming using the input from paired dataset collections: Rename output in workflow fails on paired dataset collection #1675, Rename output file on workflow #1686

[zipho]

@lparsons Do you know if that large ticket was ever created for these above proposals/feature changes?
I would like to help in getting this functionality into a milestone of some sort.

[lparsons]

@zipho Not that I know of, at least nothing other than this ticket.