Question: Need help with "Filter pileup" tool: not recognizing pileup data in "Select Dataset" popup menu
1
gravatar for arjunrajlab
4.2 years ago by
arjunrajlab20
arjunrajlab20 wrote:

I have been (roughly) following the tutorial on

https://usegalaxy.org/u/aun1/p/mtdemo-getting-things-mapped

and I'm getting stuck on the step where I have to filter the pileup.  It seems that Galaxy doesn't recognize that I have pileup data and thus I am unable to select it in "select dataset".  I have also noticed that even if I choose "set columns manually", it still doesn't give me any options under "select dataset".  Moreover, if I use "Pileup-to-interval", the data does show up, so it's not that the data itself is inherently flawed or improperly formatted.  Am I doing something really silly here?

 

Thanks, Arjun


 

Tool name: Filter pileup
Tool version: 1.0.2
Tool ID: toolshed.g2.bx.psu.edu/repos/devteam/pileup_parser/pileup_parser/1.0.2
ToolShed URL: https://toolshed.g2.bx.psu.edu/view/devteam/pileup_parser

 

filter-pileup • 1.1k views
ADD COMMENTlink modified 4.2 years ago by Jennifer Hillman Jackson25k • written 4.2 years ago by arjunrajlab20
2
gravatar for Jennifer Hillman Jackson
4.2 years ago by
United States
Jennifer Hillman Jackson25k wrote:

Hello,

Reassign the "datatype" for the input dataset so that it is recognized by the tool.
http://wiki.galaxyproject.org/Support#Tool_doesn.27t_recognize_dataset
Do this by clicking on the pencil icon in the upper right corner of the dataset. The 'Edit attributes' forms will open in the center panel. Use the tab "Datatype", change the type to "pileup", and save. Allow metadata to reset (the dataset itself may turn yellow for a bit) - all normal.

Back in the History view when done, you should see the dataset with the modified "datatype" attribute with the "format: pileup" label. And next time you use the filter tool, the dataset should show up as an input option.

Actual content of the dataset is still your responsibility, but it is known that some tools that produce pileup datasets do not label them as such - so I am guessing that is where this started.

Take care, Jen, Galaxy team

ADD COMMENTlink written 4.2 years ago by Jennifer Hillman Jackson25k
1

Thanks, that worked great!

ADD REPLYlink written 4.2 years ago by arjunrajlab20

Very glad, and appreciate the answer accept - will almost certainly help others locate the solution going forward! Jen

ADD REPLYlink written 4.2 years ago by Jennifer Hillman Jackson25k
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