I was trying to enter the 2nd fq file into the second dialog box for
tool but then the selection automatically changes to be the same as
filename in the first dialog.
is this a known issue?
NGS: Picard (beta)
BAM<https: main.g2.bx.psu.edu="" tool_runner?tool_id="picard_FastqToSam">
an unaligned BAM file
The tool will list all datasets of the appropriate input datatype in
your history, including duplicates. The two must be the same and is
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
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
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
problem and didn't notice anything off with my samples.