I put a tool: "samtools_filter" into the galaxy toolshed 
that uses   samtools view  to filter regions.   It creates symbolic links as 
Peter suggests.
(The symbolic links are created in the job_working directory which is 
automatically deleted when the job is finished.)


Hi Peter, Thanks for you quick answer! But I am very new to Galaxy. Could you 
explain something about those symlinks?
Regards, Jaap
 On Wed, Jun 20, 2012 at 2:59 PM, <j.w.f.van_der_heij...@lumc.nl> wrote:
Hi all,

I was working on the integration of the "samtools view" to work with Galaxy.
The idea is to filter an indexed bam file on a chromosome with "samtools
view -bh in.bam.bai chr1".
After some research I noted that samtools will only execute this command
when it can find the corresponding sorted bam file, so the "in.bam".

The problem is that Galaxy renames all the files. So "in.bam" will be for
instance dataset_1.dat. When I index the bam file I will get an indexed bam
file named dataset_2.dat. Samtools can't detect then that dataset_1.dat is
the sorted bam file and dataset_2.dat is the bai file.

Now I was wondering if it is possible to rename files in the
~/galaxy-dist/database/files/000 with a command line. So that dataset_2.dat
will be moved to dataset_1.dat.bai.

Does anyone know how to do that?

Kind Regards,
The simple answer is a wrapper script which makes symlinks for
the BAM file and its BAI file using the normal naming conventions.


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