Hi Michiel,

Did you finish wrapping samtools idxstats? I can't see it on the Tool Shed...

If not, I may tackle this shortly.

Peter

On Wed, May 22, 2013 at 2:39 PM, Jeremy Goecks <jeremy.goe...@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':
>
> ${input_bam.metadata.bam_index}
>
> Once you have the file path, you can set up a symbolic link to it and the 
> tool should work fine.
>
> Good luck,
> J.
>
>
>
> On May 22, 2013, at 4:05 AM, Michiel Van Bel wrote:
>
>> Hi,
>>
>> 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.
>>
>> regards,
>> Michiel
>>
>> PS: I've searched the mailing list archives for this problem but did not 
>> find any matches. Apologies if I somehow missed the answer.
>>
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