Question: Galaxy: Check input file names are the same
0
gravatar for shebna12
6 days ago by
shebna120
shebna120 wrote:

I would like to ask if it's possible to check the file name of an input dataset. I have this problem in BOWTIE wherein if there are paired reads, it will ask two inputs. I want to remove the possibility of using the same file as an input for the first set of reads and second set of reads.

example scenario of my problem:

First set of reads: reads1.fq

Second set of reads: reads1.fq

Thank you!

bowtie galaxy • 44 views
ADD COMMENTlink modified 5 days ago by Jennifer Hillman Jackson22k • written 6 days ago by shebna120
1
gravatar for Jennifer Hillman Jackson
5 days ago by
United States
Jennifer Hillman Jackson22k wrote:

Hello,

Consider placing your data into a Dataset Collection. That way you only need to pair it once correctly when using nearly any downstream tool. How to: https://galaxyproject.org/tutorials/collections/

Currently, the Bowtie2 tool will not automatically prevent the same dataset from being selected across selectable inputs. This would be a useful enhancement - I created a ticket for this here. Please feel free to add comments or to upvote. A similar enhancement was already put in place for an admin local data management function here.

Thanks! Jen, Galaxy team

ADD COMMENTlink modified 5 days ago • written 5 days ago by Jennifer Hillman Jackson22k

Thank you, Jen! As I was trying to find an answer yesterday, I thought of comparing the values of two params using the ExpressionValidator from the validation.py file but it doesn't allow two values to be accessed. Maybe I could add a DuplicatesValidator class on it but I can't figure out how to access the value of the other param.

I guess my best choice for now is wait for further updates from the Galaxy team.

ADD REPLYlink written 4 days ago by shebna120

There is an older function for the select/multi-select fields that filter out "already-selected" inputs on tool forms. I expect that this will be the final remedy. It is a global function so you won't need to include duplicate filters in your tool directly (afaik).

If you want to add use-cases, dev ideas, or other comments to the ticket I made, please do so. Upvoting will also draw attention to the request. It is a measure of community interest when setting the priority for the change.

ADD REPLYlink written 4 days ago by Jennifer Hillman Jackson22k
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