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.vandeweyer@ua.ac.be http://ua.ac.be/cognitivegenetics http://www.linkedin.com/pub/geert-vandeweyer/26/457/726
Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: