Question: Galaxy: Check input file names are the same
gravatar for shebna12
16 months ago by
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 • 518 views
ADD COMMENTlink modified 16 months ago by Jennifer Hillman Jackson25k • written 16 months ago by shebna120
gravatar for Jennifer Hillman Jackson
16 months ago by
United States
Jennifer Hillman Jackson25k wrote:


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:

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 16 months ago • written 16 months ago by Jennifer Hillman Jackson25k

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 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 16 months 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 16 months ago by Jennifer Hillman Jackson25k
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