In the tool command line template, you can do this:

${input_bam.metadata.bam_index}

to get the the location of the bai.

See the FreeBayes wrapper for an example.

Best,
J.

On Jun 29, 2012, at 10:03 AM, Geert Vandeweyer wrote:

> Hi,
> 
> I'm working on a tool that will export vcf files together with bam/bai files 
> to a long term storage location on our local installation. How can i get the 
> path to the automatically created bai file for a provided bam file? Can it be 
> derived from the file bam file path?
> 
> Best regards,
> 
> Geert Vandeweyer
> 
> -- 
> 
> Geert Vandeweyer, Ph.D.
> Department of Medical Genetics
> University of Antwerp
> Prins Boudewijnlaan 43
> 2650 Edegem
> Belgium
> Tel: +32 (0)3 275 97 56
> E-mail: geert.vandewe...@ua.ac.be
> http://ua.ac.be/cognitivegenetics
> http://www.linkedin.com/pub/geert-vandeweyer/26/457/726
> 
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