Did you finish wrapping samtools idxstats? I can't see it on the Tool Shed...
If not, I may tackle this shortly.
On Wed, May 22, 2013 at 2:39 PM, Jeremy Goecks <jeremy.goecks(a)emory.edu> wrote:
Galaxy stores a BAI for each BAM internally; you can access it in a
tool wrapper like this (assuming the name of your input dataset is 'input_bam':
Once you have the file path, you can set up a symbolic link to it and the tool should
On May 22, 2013, at 4:05 AM, Michiel Van Bel wrote:
> I would like to inquire whether anyone has attempted to implement the idxstats tool
from samtools into Galaxy?
> The xml-file for idxstats is not present in the Galaxy source code, which led me to
try and implement it myself.
> However, the main problem I face is that the idxstats tool silently relies on having
an index file available (within the same directory) for the bam file you which to print
the stats for.
> E.g. samtools idxstats PATH/test.bam
> searches for PATH/test.bam.bai and gives an error when this file is not present. And
somehow I cannot model this behavior in Galaxy.
> A different solution would of course be to ask the author(s) of samtools to have an
option available where the user can directly indicate the path to the index file.
> PS: I've searched the mailing list archives for this problem but did not find any
matches. Apologies if I somehow missed the answer.