Thanks! Got it to work
FYI
The data type was labelled as fastqcsanger although the extension
wasn't .fq (was
.fq_1) but it was listed in the first pull down menu

after I renamed it to .fq for both files, the second option didn't
automatically change to the first fastq file already.

Cheers
Kevin


On 22 October 2012 14:47, Jennifer Jackson <j...@bx.psu.edu> wrote:

> Hello,
>
> The tool will list all datasets of the appropriate input datatype in your
> history, including duplicates. The two must be the same and is set by the
> first dataset. For example, if the first is assigned as simply .fastq, the
> the second must be also be .fastq (and only .fastq datasets will be listed
> as potential inputs). If the first is .fastqsanger, the second must also be
> .fastqsanger.
>
> Modify datatypes as needed using the pencil icon -> Edit datasets ->
> Datatypes tab. Or, you may wish to use the "FASTQ Groomer" tool, if the
> data needs to be scaled to be Phred+33 (datatype .fastqsanger) - a format
> required by most of Galaxy's analysis tools. Please see the "FASTQ Groomer"
> tool form for the details. Data already scaled to Phred+33 can be safely
> set to .fastqsanger without running the groomer tool, although it can be
> helpful (option would be "Sanger") if you suspect a format issue, as it
> reports exactly where in the file the problem is located in the error
> message, but leaves the data unchanged (even when successful, e.g. no
> errors found).
>
> Hopefully this helps, but if your question has been misunderstood, please
> let us know, as we will probably need to examine your exact history/run
> conditions. I did quickly run a small test to check for a UI problem and
> didn't notice anything off with my samples.
>
> Best,
>
> Jen
> Galaxy team
>
>
> On 10/21/12 7:38 PM, Kevin L wrote:
>
>> Hi
>> I was trying to enter the 2nd fq file into the second dialog box for
>> this tool but then the selection automatically changes to be the same as
>> the filename in the first dialog.
>>
>> is this a known issue?
>>
>> NGS: Picard (beta)
>> CONVERSION
>> FASTQ to BAM
>> <https://main.g2.bx.psu.edu/**tool_runner?tool_id=picard_**FastqToSam<https://main.g2.bx.psu.edu/tool_runner?tool_id=picard_FastqToSam>>
>> creates
>> an unaligned BAM file
>>
>>
>> ______________________________**_____________________________
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> --
> Jennifer Jackson
> http://galaxyproject.org
>
___________________________________________________________
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