Hi Jacqui,
The "NGS: SAM Tools -> Filter pileup" tool was corrected last September to require input datasets to be assigned to the format "pileup". Is there a chance that these datasets are not? Maybe imported or manipulated by other tools, resulting in another datatype assignment (tabular or other)? The datatype is noted directly under the dataset name, in each dataset's box in the history.
If so, you can reassign the format (as long as it meets specification, see the tool "NGS: SAM Tools -> Generate pileup" for a description), by clicking on the pencil icon for a dataset, then the tab "Datatype", and assigning "pileup" manually (don't forget to save). This will help with tool->input dataset recognition.
Should the problem be unrelated to file format, please send in a link to a shared history (on the public Main server) and we can help to troubleshoot from there. You can send this directly to me. From the history panel use: Options (gear icon) -> Share or Publish -> generate link -> copy/paste into email.
Best,
Jen Galaxy team
On 11/22/12 3:16 AM, Jacqui Stockley wrote:
Hi,
I was wondering if you could help me with a problem I have been having recently. I have carried out a number of NGS analyses using SAM Tools where I have generated pileup and then filtered this file using the filter pileup tool. However, recently when I have tried to do this the filter pileup is not recognising a compatible dataset in the history (ie it is not recognising the generate pileup file). I have always done the same so I can't understand what I might have done wrong. I have gone into old datasets and tried to filter pileups from previous histories and they also do not recognise the generate pileup file despite the fact they have previously!
Is there something I am doing majorly wrong or should I be using another function?
Many thanks for any help or advice!
Jacqui
The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list:
http://lists.bx.psu.edu/listinfo/galaxy-dev
To manage your subscriptions to this and other Galaxy lists, please use the interface at: