Hai Galaxy Team, I have created a .sam file using my own tool. I used a custom genome that I added to the bowtie_indices.loc. I want to create another tool which will contain 3 steps, 1. samtool view (sam to bam conversion) 2. samtool sort (sorting bam file) 3. samtool index (creating .bai file) My problem is how the galaxy can know about the index(.bai) file I am creating?

From one of the mailing list I learn that a bai file is automatically created when adding a bam file to the history. http://dev.list.galaxyproject.org/question-about-bam-and-bai-td4136797.html

So can I skip the 3rd step(samtool index)? ie,Whether a .bai file will create automatically when the tool create the sorted bam file? If yes,where will be the .bai file? Regards, Deepthi.