Hi Peter,

Thanks for the thoughtful comments. I believe the requirement for the genome was imposed by the use of an underlying BedTools utility. I also think that in a newer version of that tool, the requirement was removed, since you correctly point out it is not really necessary.

I will see if I can update the tool to remove that requirement and also see about changing the tool id. Sorry for the conflict, that was an oversight on my part, though it would be nice if the Tool Shed could check and warn when someone tries to create a new tool. I would suggest flagging the new repo as invalid until the id is updated instead of outright rejection.

As for the author info, you're right, I should really add that as well. That tool was put together very quickly to meet the need of a customer and I didn't properly clean things up before I uploaded. I'll let you know once I get an update out. Of course, any patches etc. are welcome. ;-)

Lance

Peter Cock wrote:
Hi Brad&  Lance,

I've been using Brad's bam_to_bigwig tool in Galaxy but realized
today (with a new dataset using a splice-aware mapper) that it
doesn't seem to be ignoring CIGAR N operators where a read is
split over an intron. Looking over Brad's Python script which
calculates the coverage to write an intermediate wiggle file, this is
done with the samtools via pysam. It is not obvious to me if this
can be easily modified to ignore introns. Is this possible Brad?

I wasn't aware of Lance's rival bam_to_bigwig tool in the ToolShed
till now, and that does talk about this issue. It has a boolean option
to ignore gaps when computing coverage, recommended for
RNA-Seq where reads are mapped across long splice junctions.

Lance, from your tool's help it sounds like it needs a genome
database build filled in. I don't understand this requirement - Brad's
tool works just fine for standalone BAM files (for example reads
mapped to an in house assembly). Is that not supported in your
tool?

Galaxy team - why does the ToolShed allow duplicate repository
names (here bam_to_bigwig) AND duplicate tool IDs (again, here
bam_to_bigwig)? Won't this cause chaos when sharing workflows?
I would suggest checking this when a tool is uploaded and rejecting
repository name or tool ID clashes.

Regards,

Peter

P.S.

Brad, your tool is missing an explicit<requirements>  tag
listing the UCSC binary wigToBigWig, and the Python library
pysam.

Lance, your tool doesn't seem to include any author information
like your name or email address. I'm inferring it is yours from the
Galaxy tool shed user id, lparsons.

--
Lance Parsons - Scientific Programmer
134 Carl C. Icahn Laboratory
Lewis-Sigler Institute for Integrative Genomics
Princeton University

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