Hi Andrew,

If you want to run the tool "Filter pileup on coverage and SNPs" on dataset #21, change the datatype to be "pileup". Then it will show up under the list of inputs. Be sure to set the forms options for a 10-column pileup input when you run it.


Change the datatype by clicking on the pencil icon for the dataset, to open the Edit Attributes form in the center panel. Click on the "Datatype" tab, then enter pileup, select it from the list, and save. Allow the metadata to finish detecting on it's own.

Hopefully this helps,

Jen
Galaxy team

On 6/24/13 5:11 PM, Andrew Guo wrote:
This is on the public instance. I can share my history with you right here...

https://main.g2.bx.psu.edu/u/guotaek/h/galaxy-101


On Mon, Jun 24, 2013 at 6:40 PM, Jennifer Jackson <j...@bx.psu.edu <mailto:j...@bx.psu.edu>> wrote:

    Hi Andrew,

    Is this on a local instance or the public Main Galaxy instance at
    usegalaxy.org <http://usegalaxy.org> (https://main.g2.bx.psu.edu)?

    Also, the exact tools being used and the order is not clear. Maybe
    a step is missing from what is listed? (I am just guessing) If you
    are using the public Main instance, you can share a history with
    me and I can provide feedback. If this is on your instance, could
    you list the tools by name, in the order used, with key parameters
    (e.g. "Generate pileup from BAM dataset" with option 10-column
    pileup)?

    It sounds like there might be a mix-up about the file formats
    being used as inputs to tools. It may be something that can be
    resolved by reassigning the datatype or by adjusting the tool(s) used.

    Best,

    Jen
    Galaxy team


    On 6/24/13 1:10 PM, Andrew Guo wrote:
    After using tools to convert a SAM to a BAM file, I am trying to
    filter the BAM pileup. However, the filter BAM tool is not
    picking up on the dataset that I just created. It should show up
    under 10 column pileup, but an error message is saying "History
    does not include a dataset of the required format/build". Could
    you provide any insight into this?

    Thanks,
    Andrew


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-- Jennifer Hillman-Jackson
    Galaxy Support and Training
    http://galaxyproject.org



--
Jennifer Hillman-Jackson
Galaxy Support and Training
http://galaxyproject.org

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