Need help with "Barcode Splitter" tool

Question: Need help with "Barcode Splitter" tool

4.0 years ago by

United States

tymiller • 60 wrote:

Hi,

I would like to use the new "enhanced" barcode splitter that was developed this past year. It is in the Galaxy Main toolshed, but not available to use in workflows on Galaxy Main. It is basically the same thing, but gives the option to directly import the output files to a new history, preventing the user from having to download and upload each file individually (very helpful when looking at multiplexed data with 45 barcodes, like I am doing now).

Would it be possible to add this tool in place or in addition to the Barcode Splitter tool now available on Galaxy Main? Searching through BioStar, this seems like a frequent question and would be helpful for many researchers! It can be found here: https://toolshed.g2.bx.psu.edu/view/lparsons/fastx_barcode_splitter_enhanced

In addition, ideally, there would be a way to output the split files directly into the next step in the workflow. Is there anyway to do this? For example, if someone had 10 files coming from the Barcode Splitter step in the workflow, is there a way to send those files directly into the next step, for example a Trim step?

Thanks!!

Tyler

Tool name: Barcode Splitter
Tool version: 1.0.0
Tool ID: toolshed.g2.bx.psu.edu/repos/devteam/fastx_barcode_splitter/cshl_fastx_barcode_splitter/1.0.0
ToolShed URL: https://toolshed.g2.bx.psu.edu/view/devteam/fastx_barcode_splitter

barcode-splitter • 1.3k views

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modified 4.0 years ago by Lance Parsons • 110 • written 4.0 years ago by tymiller • 60

4.0 years ago by

Lance Parsons • 110

United States

Lance Parsons • 110 wrote:

I wrote the enhanced version of the barcode splitter tool to meet our own institutional needs, but I'm glad you find the enhancements useful. I can't speak to the plans of the Galaxy team to install things like that on Main, however, I've had similar frustrations about using the tool in a workflow. Since the tool was written, there have been many enhancements to the tool and workflow framework including the ability to run workflows on multiple files, etc. Does anyone on the Galaxy team have any insight into how we might be able to modify the tool to allow it to be used in workflows? The main issue that the number of output files depends on the number of barcodes in one of the input files and thus is not known apriori (but could be determined easily and quickly).

ADD COMMENT • link written 4.0 years ago by Lance Parsons • 110

Looks like this Trello card (https://trello.com/c/ndVQmt3G) covers functionality that should make this possible. I'll track it and try to get the tool updated once the new functionality is released.

ADD REPLY • link written 4.0 years ago by Lance Parsons • 110

I'm working on a project that would really benefit from using the barcode splitter tool in its workflow as well - do you happen to know if this is available yet?

ADD REPLY • link written 3.4 years ago by mccoykg • 80

As far as I know, its still not available. I ended up just copying all the links into excel, using a macros to display the entire link url and then copy and pasting them into the "Get Data" "Upload". Not perfect but relatively efficient

ADD REPLY • link written 3.4 years ago by tymiller • 60

Thanks, I'll try that!

ADD REPLY • link written 3.4 years ago by mccoykg • 80

I used visual basic and this was code Sub ExtractHL() Dim HL As Hyperlink For Each HL In ActiveSheet.Hyperlinks HL.Range.Offset(0, 1).Value = HL.Address Next End Sub

ADD REPLY • link written 3.4 years ago by tymiller • 60

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