On Thu, Feb 10, 2011 at 12:49 PM, Stephen Taylor
<stephen.tay...@imm.ox.ac.uk> wrote:
>
> I think you have but it doesn't help. :-)
>
> The issue is we get a lot of Illumina 1.3+ format FASTQ files and bowtie in
> Galaxy by default doesn't accept them although there is an option on the
> command line bowtie to read these. So I think the solution seems to be
> either hardwire the code in our local Galaxy instance to use the
> --solexa1.3-quals option or (probably more useful) put a drop down list in
> the web UI to allow the user to set the format of the fastq sequences on the
> bowtie tool.
>

Not the best approach.

I think you should update the XML to include the --solexa1.3-quals option
if the Galaxy file format is fastqillumina, see for example (in the reverse
situation) the -Q 33 option is only used on fastqsanger when calling
the FASTX tools, e.g.

https://bitbucket.org/galaxy/galaxy-central/src/default/tools/fastx_toolkit/fastx_clipper.xml

That way the user must mark their FASTQ file type as usual (at upload time
or via the "pencil icon" to edit the attributes), and then bowtie will be called
appropriately.

Peter
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